title: Elijah_ribo-_BS

data_processing:
Raw sequencing reads were processed by Cutadapt (v.4.2) to remove low-quality bases (-q 20) and short reads (-m 18), as well as to trim adaptors. 6mer UMI were extracted by UMI-tools extract (v.1.0.1) and used for deduplication. Paired reads were then merged into single reads using fastp (v.1.0.1).
Reads were aligned to Epstein-Barr virus (EBV) genome, strain B95-8 (V01555.2)
The aligned reads were then filtered and sorted using samtools (v.1.16.1). Mutations are counted by samtools mpileup (v.1.16.1) and cpup (v.0.1.0) (https://github.com/y9c/cpup).
Assembly: hg38
Supplementary files format and content: Excel table showing the comparision of Psi sites detected.

source_name: Elijah

growth_protocol: Raji, and Elijah cells were grown in Roswell Park Memorial Institute 1640 medium (RPMI 1640) (Thermo), complemented with 10% (v/v) fetal bovine serum (FBS) (Biosera), 2 mM L-glutamine (Thermo), and 100 units/ml penicillin and 100 µg/ml streptomycin (Thermo). Cells were grown in humidified incubator at 37 °C with 5% CO2. Raji and Elijah cell lines were gifted from Prof. Paul Farrell (Imperial College London). Cell lines were monthly tested for mycoplasma using MycoAlert Kit (Lonza) and were sent for authentication by Eurofins genomics.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) and Direct-zol RNA Miniprep Plus (Zymo Research) according to the manufacturer’s protocol. Ribo- RNA was isolated using RiboMinus Eukaryote System v2 (Invitrogen) according to the manufacturer’s protocol. PolyA+ RNA was isolated by two rounds of polyA-tailed selection using Dynabeads mRNA DIRECT Purification Kit (Invitrogen) according to the manufacturer’s protocol. To remove genomic DNA contamination, RNA was then treated with Turbo DNase and purified by Zymo-IC Column with RNA binding buffer.
Library construction of modified BID-seq was conducted similarly with BACS except for the chemical conversion step. For BS treatment, revised BS and desulphonation reaction conditions of BID-seq were used. Briefly, the 3’-ligated RNA was eluted in 10 μl nuclease-free H2O. An 8.5 μl aliquot was subjected to modified BID-seq library construction, while the remaining 1.5 μl was saved as control sample. The 8.5 μl aliquot was mixed with 45 μl freshly prepared BS reagent (2.4 M Na2SO3 and 0.36 M NaHSO3, Sigma) and incubated at 70 °C for 3 h. The treated RNA was purified by Zymo-IC Column with RNA binding buffer. In-column desulphonation was performed using RNA desulphonation buffer (Zymo), with the column incubated at room temperature for 75 min.

value: Elijah

tag: treatment

value: BS


title: Raji_ribo-_BS

status: Public on Jul 31 2024

type: SRA

city: Oxford

first: Linzhen

last: Kong

address: University of Oxford Old Road Campus Research Building

department: Nuffield Department of Medicine

country: United Kingdom

institute: Ludwig Institute for Cancer Research

library_source: other

molecule: other

organism: Homo sapiens

source_name: Raji

tag: cell line

value: Raji


title: Elijah_ribo-_ctrl

value: control


title: N3-RT11-83

city: Philadelphia

first: Huasheng

last: Yu

state: PENNSYLVANIA

address: 3610 Hamilton Walk

department: Neuroscience

country: USA

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
Raw sequencing data was demultiplexed with bcl2fastq2 v.2.20 (Illumina)
Demultiplexed data was trimmed with Cutadapt to remove Tn5 transposon adapter sequences.
The trimmed data were aligned to human genome using STAR v.2.7.9a49.
STAR quantMode GeneCounts was used to quantify unique mapped reads to gene counts.
Gene counts file was used for the downstream analysis
Assembly: human genome (GRCh38 GENCODE as the reference genome, and GRCh38.104. GTF as the annotation)
Supplementary files format and content: Comma-separated file includes raw counts for each Sample

molecule: total RNA

source_name: Dorsal root ganglia

extract_protocol:
Human DRG tissues were procured from National Disease Research Interchange (NDRI). The research application was approved by the NDRI Feasibility Committee (RLUW1 01). Six DRGs between T11 to L5 of three human donors aged from 23- 61 years were used in this study. The dissected DRG tissues from human donors were immediately imbedded in OCT, shipped to the Luo lab on dry ice and stored in -80 ℃ until use. The information of DRGs and dis-identified donors and screening criteria are summarized in the manuscript Supplementary Tables 1 & 2. The hDRGs imbedded in OCT were cryosectioned (Cryostat Leica Cm1950) into 20 μm sec-tions and mounted onto Arcturus PEN Membrane Frame Slides (Applied biosystems, LCM0521). One of every five consecutive sections was collected for laser capture microdissec-tion to avoid repeated dissection of the soma from the same neuron in different sections. The slides were stored in -80 ℃ until further use.On the day of laser capture microdissection, the slides were transferred to the SBDRC laser capture microdissection (LCM) core on dry ice. Before dissection, the section was briefly stained with RNase free Arcturus™ Histogene™ staining solution (Applied biosystems, 12241-05) for better visualization of neuronal soma: 70% cold EtOH for 30s; Histogene™ staining for 10s; 70% cold EtOH for 30s; 95% cold EtOH for 30s; 100% cold EtOH for 30s and air dry for 2min. Then, the slide was put onto laser capture microdissection microscope system (Leica LMD6) for the neuronal soma dissection. The laser was calibrated, and the laser intensity was adjusted to achieve best dissection efficiency. The dissected individual neuronal soma was col-lected in the cap of a 200 μl PCR tube containing 4 μl lysis buffer.
The sequencing library was generated following Smart-seq2 workflow. The libraries passing through all quality con-trols were selected for the final sequencing.

tag: tissue

value: Dorsal root ganglia

tag: donor id

tag: age(years)

tag: race

value: Caucasian

tag: gender

value: Female

tag: region

value: thoracic 11

tag: sequencing batch

tag: dissected soma size

tag: cell identity


title: PBMC RNA, High Blood Pressure, H22

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
The bioinformatic pipeline for the samples sequenced using BGI500 includes, (i) the elimination of the low-quality reads, adaptors and other contaminants to get clean reads. The elimination includes 5' primer contaminants, no-insert tags, oversized insertion tags, low-quality tags, poly A tags, and small tags, tags without 3' primer. The low-quality tags are those which have more than four bases and whose quality is less than ten, or those which have more than six bases and have a quality less than thirteen. (ii) Next the length distribution of clean tags is then summarized. Normally, the length distribution of small RNA is between 18nt and 30nt (miRNA -21nt or 22nt, siRNA -24nt, and piRNA - 30nt). (iii)After filtering, the remaining tags are called clean tags and stored in FASTQ format. (iv) Bowtie was used to map clean reads to the reference genome and to other sRNA databases (cmsearch was used for Rfam)19,20. In the annotation information of different RNAs, to avoid mapping of sRNA to multiple categories, priority rule was followed: miRNA > piRNA > snoRNA > Rfam > other sRNA. The small RNA expression level was calculated by using Transcripts Per Kilobase Million (TPM).  The TPM method eliminates the influence of sequencing discrepancy on the calculation of small RNA expression level. Therefore, the calculated gene expression level data can be used directly to compare the difference in gene expression between the samples. To calculate the TPM the following formula is used: TPM=(C*106 )/N. DESeq2 based on the negative binomial distribution, was performed as described at Michael I, et al. We used 'Adjusted Pvalue ≤ 0.1 and the absolute value of Log2Ratio ≥ 1' as the default threshold to judge the significance of gene expression difference.
Assembly: hg19_UCSC_20180822
Supplementary files format and content: The processed file is in Excel format and contains TPM.
Supplementary files format and content: The processed file is in Excel format and contains  log2fc, qvalue, p value for the respetive genes with their gene symbol, gene ID and other gene related informations.

source_name: Blood

extract_protocol:
Peripheral Blood samples (2.5 ml) were drawn from each volunteer in a PAXgene tube (Qiagen cat# 762165) followed by total RNA (including miRNA) isolation using a commercial kit (Qiagen cat# 763134) according to the manufacturer instruction. Total RNA concentration and quality were evaluated using a nanodrop system (ThermoFisher Scientific).
The experiment pipeline for library preparation for small RNA sequencing includes (i) separation of 18-30nt RNA segment by PAGE gel, (ii)3' adaptor ligation to link 5-adenylated 3-blocked single-stranded DNA adapter to 3' end of selected small RNAs, (iii)reverse primer annealing using a RT primer which is cross-linked to the 3’-adapter sequence of RNA and excess 3’adapter followed by (iv) 5' adaptor ligation, (v) cDNA synthesis, (vi)PCR amplification to enrich cDNA with both 3' and 5' adaptor, (vii)library fragment selection by separation of the PCR product of 100~120bp by PAGE gel to eliminate primer-dimer and other byproducts, (viii) library quantitative and pooling cyclization followed by (ix)sequencing using BGISEQ-500 technology.

value: Blood

tag: cell type

value: Peripheral blood mono nuclear cells


title: PBMC RNA, High Blood Pressure, H21


title: LNCaP-Methanol, native, scATAC

city: TAMPA

first: Liang

last: Wang

state: FL

address: 14059 Riveredge Drove

institute: Moffitt Cancer Center

description:
LNCaP-Methanol_barcodes.tsv
LNCaP-Methanol_features.tsv
LNCaP-Methanol_matrix.mtx

library_source: genomic single cell

data_processing:
To demultiplex the multiome samples and generate the FASTQ files for the single-cell quantification, we used Cellranger-ARC mkfastq to perform raw base calling from both ATAC and RNA flow cells. With the FASTQ files ready, we then used Cellranger-ARC count to perform sequencing alignment, cell barcode quantification, ATAC-seq peak calling, and RNA-seq gene expression quantification. After the counting process, we obtained the feature-barcoding matrices, the ATAC-seq fragment and peak information, and other intermediate  for downstream multiome association analysis.
Assembly: GRCh38
Supplementary files format and content: Cell barcode (_barcodes.tsv) : qualified single-cell identity barcode; Genes and peaks (_features.tsv) : RNA-seq gene name and ATAC-seq peak information; Data matrix (_matrix.mtx) : feature barcoded matrices

molecule: genomic DNA

source_name: Prostate

extract_protocol:
The multiome libraries were prepared according to the manufacturer’s protocol. Briefly, nuclei were isolated from the dissociated cells and the open chromatin regions were tagged with Tn5 transposase. The tagmentated nuclei of each cell line was then applied to one lane of the Chromium Next GEM Chip J for GEM generation and molecule barcoding. After GEM incubation and library construction, each ATAC-seq read was labeled with a 10x cell identity barcodes, while each RNA-seq read was captured by a paired barcodes with an Unique Molecular Identifier (UMI). For raw multiome library capture, we aimed 8,000-10,000 nuclei for each sample and 25,000 scATAC-seq, and 20,000 scRNA-seq reads per cell to ensure the data coverage. We aimed for similar total read count for each targeted enriched library for better comparisons.
After GEM incubation and library construction, each ATAC-seq read was labeled with a 10x cell identity barcodes, while each RNA-seq read was captured by a paired barcodes with an Unique Molecular Identifier (UMI).
For raw multiome library capture, we aimed 8,000-10,000 nuclei for each sample and 25,000 scATAC-seq, and 20,000 scRNA-seq reads per cell to ensure the data coverage. We aimed for similar total read count for each targeted enriched library for better comparisons.

value: Prostate

value: LNCaP

value: Human Prostate Cancer Cells


title: PBMC RNA, High Blood Pressure, H23


title: LNCaP-Methanol, native, scRNA

library_source: transcriptomic single cell

molecule: nuclear RNA


title: PBMC RNA, High Blood Pressure, H20


title: N3-RT11-84

value: hPropr


title: Raji_ribo-_ctrl


title: N3-RT11-82


title: N3-RT11-81


title: LNCaP-DHT, native, scRNA

description:
LNCaP-DHT_barcodes.tsv
LNCaP-DHT_features.tsv
LNCaP-DHT_matrix.mtx


title: N3-RT11-80


title: 22Rv1-DHT, native, scRNA

description:
22Rv1-DHT_barcodes.tsv
22Rv1-DHT_features.tsv
22Rv1-DHT_matrix.mtx


title: 22Rv1-Methanol, native, scATAC

description:
22Rv1-Methanol_barcodes.tsv
22Rv1-Methanol_features.tsv
22Rv1-Methanol_matrix.mtx


title: N3-RT11-85


title: PBMC RNA, High Blood Pressure, H18


title: RWPE2, native, scATAC, rep2

description:
RWPE2R2_barcodes.tsv
RWPE2R2_features.tsv
RWPE2R2_matrix.mtx


title: RWPE2, native, scRNA, rep2


title: LNCaP-DHT, native, scATAC


title: N3-RT11-78


title: RWPE2, native, scATAC, rep1

description:
RWPE2R1_barcodes.tsv
RWPE2R1_features.tsv
RWPE2R1_matrix.mtx


title: N3-RT11-77


title: RWPE1, native, scATAC, rep1

description:
RWPE1R1_barcodes.tsv
RWPE1R1_features.tsv
RWPE1R1_matrix.mtx

value: Human Prostate Epithelial Cells


title: RWPE2, native, scRNA, rep1


title: PBMC RNA, High Blood Pressure, H16


title: RWPE1, native, scRNA, rep2

description:
RWPE1R2_barcodes.tsv
RWPE1R2_features.tsv
RWPE1R2_matrix.mtx


title: 22Rv1-DHT, native, scATAC


title: PC3, native, scATAC

description:
PC3_barcodes.tsv
PC3_features.tsv
PC3_matrix.mtx


title: PBMC RNA, High Blood Pressure, H14


title: PBMC RNA, High Blood Pressure, H19


title: PBMC RNA, High Blood Pressure, H15


title: N3-RT11-76


title: RWPE1, native, scATAC, rep2


title: PC3, native, scRNA


title: N3-RT11-74


title: RWPE1, native, scRNA, rep1


title: 22Rv1-Methanol, native, scRNA


title: PBMC RNA, High Blood Pressure, H17


title: N3-RT11-79


title: PBMC RNA, High Blood Pressure, H12


title: PBMC RNA, High Blood Pressure, H28


title: N3-RT11-73


title: DU145, native, scRNA

description:
DU145_barcodes.tsv
DU145_features.tsv
DU145_matrix.mtx


title: DU145, native, scATAC


title: BPH1, native, scATAC

description:
BPH1_barcodes.tsv
BPH1_features.tsv
BPH1_matrix.mtx


title: PBMC RNA, High Blood Pressure, H11


title: BPH1, native, scRNA


title: N3-RT11-75


title: PBMC RNA, High Blood Pressure, H13


title: N3-RT11-72


title: PBMC RNA, High Blood Pressure, H10


title: PrEC, native, scATAC

description:
PrEC_barcodes.tsv
PrEC_features.tsv
PrEC_matrix.mtx

value: PrEC


title: PrEC, native, scRNA


title: PBMC RNA, High Blood Pressure, H9


title: LNCaP-Methanol, enriched, scATAC

description:
LNCaP-Methanole_barcodes.tsv
LNCaP-Methanole_features.tsv
LNCaP-Methanole_matrix.mtx


title: LNCaP-DHT, enriched, scATAC

description:
LNCaP-DHTe_barcodes.tsv
LNCaP-DHTe_features.tsv
LNCaP-DHTe_matrix.mtx


title: PBMC RNA, High Blood Pressure, H8


title: N3-RT11-69


title: 22Rv1-DHT, enriched, scATAC

description:
22Rv1-DHTe_barcodes.tsv
22Rv1-DHTe_features.tsv
22Rv1-DHTe_matrix.mtx


title: LNCaP-Methanol, enriched, scRNA


title: N3-RT11-68


title: 22Rv1-DHT, enriched, scRNA


title: 22Rv1-Methanol, enriched, scATAC

description:
22Rv1-Methanole_barcodes.tsv
22Rv1-Methanole_features.tsv
22Rv1-Methanole_matrix.mtx


title: N3-RT11-71


title: PBMC RNA, High Blood Pressure, H6


title: PBMC RNA, High Blood Pressure, H7


title: 22Rv1-Methanol, enriched, scRNA


title: N3-RT11-67


title: RWPE2, enriched, scATAC, rep2

description:
RWPE2R2e_barcodes.tsv
RWPE2R2e_features.tsv
RWPE2R2e_matrix.mtx


title: PBMC RNA, High Blood Pressure, H5


title: N3-RT11-66


title: RWPE2, enriched, scRNA, rep2


title: RWPE2, enriched, scATAC, rep1

description:
RWPE2R1e_barcodes.tsv
RWPE2R1e_features.tsv
RWPE2R1e_matrix.mtx


title: PBMC RNA, High Blood Pressure, H4


title: RWPE2, enriched, scRNA, rep1


title: N3-RT11-65


title: LNCaP-DHT, enriched, scRNA


title: RWPE1, enriched, scATAC, rep1

description:
RWPE1R1e_barcodes.tsv
RWPE1R1e_features.tsv
RWPE1R1e_matrix.mtx


title: N3-RT11-64


title: RWPE1, enriched, scRNA, rep1


title: PBMC RNA, High Blood Pressure, H3


title: RWPE1, enriched, scRNA, rep2

description:
RWPE1R2e_barcodes.tsv
RWPE1R2e_features.tsv
RWPE1R2e_matrix.mtx


title: RWPE1, enriched, scATAC, rep2


title: PBMC RNA, High Blood Pressure, H2


title: PC3, enriched, scRNA

description:
PC3e_barcodes.tsv
PC3e_features.tsv
PC3e_matrix.mtx


title: PC3, enriched, scATAC


title: N3-RT11-62


title: DU145, enriched, scATAC

description:
DU145e_barcodes.tsv
DU145e_features.tsv
DU145e_matrix.mtx


title: N3-RT11-61


title: PBMC RNA, High Blood Pressure, H1


title: N3-RT11-63


title: N3-RT11-60


title: PBMC RNA, Elevated/Mid Blood Pressure, M17


title: BPH1, enriched, scATAC

description:
BPH1e_barcodes.tsv
BPH1e_features.tsv
BPH1e_matrix.mtx


title: PrEC, enriched, scATAC

description:
PrECe_barcodes.tsv
PrECe_features.tsv
PrECe_matrix.mtx


title: N3-RT11-70


title: PrEC, enriched, scRNA


title: PBMC RNA, Elevated/Mid Blood Pressure, M16


title: PBMC RNA, Elevated/Mid Blood Pressure, M18


title: BPH1, enriched, scRNA


title: N3-RT11-59


title: scRNA-seq_Dn6 PBMC of healthy donors

city: Tomsk

first: Irina

last: Larionova

state: Tomsk oblast

address: Lenin Ave, 36, Tomsk, Tomsk Oblast, Russia

country: Russia

institute: Tomsk State University

description: Healthy control

data_processing:
Basic processing of raw sequencing data, including quality control, read alignment, and count gene-barcode matrix, was performed in Cell Ranger 7.1.0 using human genome reference GRCh38-2020-A with default parameters
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Peripheral blood mononuclear cells

extract_protocol:
The peripheral blood mononuclear cells (PBMCs) were separated from whole blood by density gradient centrifugation using Lymphosep, Lymphocyte Separation Media (#L0560-500, Biowest, France), 1.077 g/ml density, at 600g for 30 minutes. PBMCs were washed twice with DPBS without calcium and magnesium at 300 g for 10 minutes and counted using CytoFLEX flow cytometer (Beckman Coulter, USA). 1 000 000 PBMCs were used to prepare cell suspension for single-cell sequencing. Cells were put into 1.5 ml cryo tubes and mixed with 500 μl of X-VIVO™ 10 Medium (#180989, Lonza, Switzerland), 400 μl of fetal bovine serum (#10500064, ThermoFisher Scientific, USA), and 100 μl of dimethyl sulfoxide (#F135, Paneco, Russia). Subsequently, the cell suspension was stored in cryo container at -80°C for 48 hours, and then stored in liquid nitrogen until further experiments (but not more than 6 months).
Single-cell RNA sequencing was performed on the Chromium X platform, using the 10х Genomics Chromium Next GEM Single Cell 3′ Reagent Kit v3.1. (10х Genomics, USA). Prior to library preparation, cells were counted and quality of samples was assessed. Up to 8000 cells were used for further manipulations. cDNA amplification and library construction were conducted following the manufacturer’s protocol.

value: Peripheral blood mononuclear cells

tag: Sex

value: F

tag: disease

value: Healthy control


title: PBMC RNA, Elevated/Mid Blood Pressure, M15


title: N3-RT11-58


title: scRNA-seq_Dn5 PBMC of healthy donors

description: Healthy control


title: PBMC RNA, Elevated/Mid Blood Pressure, M14


title: N3-RT11-57


title: PBMC RNA, Elevated/Mid Blood Pressure, M13


title: scRNA-seq_Dn1 PBMC of healthy donors

description: Healthy control


title: N3-RT11-56


title: scRNA-seq_Ov6 PBMC of HGSOC patients

description: Patients had debulking surgery without upfront NACT

value: High-grade serous ovarian cancer

value: Treatment-naive


title: N3-RT11-55

value: Dorsal root ganglia


title: PBMC RNA, Elevated/Mid Blood Pressure, M12


title: scRNA-seq_Ov4 PBMC of HGSOC patients

description: Patients received platinum-based neoadjuvant chemotherapy (NACT) [carboplatin plus paclitaxel] prior to surgery

value: NACT-treated


title: scRNA-seq_Dn4 PBMC of healthy donors

description: Healthy control


title: N3-RT11-54

value: Caucasian

value: Female


title: scRNA-seq_Ov5 PBMC of HGSOC patients


title: HepG2_HDV_control

data_processing:
Raw sequencing reads were processed by Cutadapt (v.4.2) to remove low-quality bases (-q 20) and short reads (-m 18), as well as to trim adaptors. 6mer UMI were extracted by UMI-tools extract (v.1.0.1) and used for deduplication. Paired reads were then merged into single reads using fastp (v.1.0.1).
Cleaned reads were first mapped to synthetic spike-ins and rRNA references using bowtie2 (v.2.4.4). The key parameters are as follows: bowtie2 -p 2 --no-unal --local -L 16 -N 1 --mp 4. The unaligned reads were subsequently mapped to snoRNA references and then to tRNA references, using the same parameters. Human snoRNA sequences that belong to HGNC “Small nucleolar RNAs” gene group were downloaded from RefSeq. Duplicate snoRNA sequences were removed. High-confidence human tRNA sequences (hg38) were downloaded from GtRNAdb. Only non-redundant tRNA sequences were kept and appended with a “3’-CCA” end. Finally, unmapped reads were aligned to human genome (hg38) with GENCODE v.43 annotation by STAR (v.2.7.9a)
The aligned reads were then filtered and sorted using samtools (v.1.16.1). For synthetic spike-ins and rRNA, only reads with MAPQ ≥10 were kept. For snoRNA and tRNA, only reads with MAPQ ≥1 were kept. For mRNA, only uniquely mapped reads (-q 30) with a maximum of 3 mutation counts were kept. Deduplication was performed using UMI-tools dedup (v.1.0.1).. Finally, mutations are counted by samtools mpileup (v.1.16.1) and cpup (v.0.1.0) (https://github.com/y9c/cpup).
Assembly: hg38
Supplementary files format and content: Excel tables show the ψ list

growth_protocol: HeLa cells were cultured in DMEM medium (Gibco) supplemented with 10% (v/v) FBS (Gibco) and 1% penicillin/streptomycin (Gibco) at 37 °C with 5% CO2. For isolation of RNA, cells were harvested by centrifugation for 5 min at 1,000× g and room temperature.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) and Direct-zol RNA Miniprep Plus (Zymo Research) according to the manufacturer’s protocol. Ribo– RNA was isolated using RiboMinus Eukaryote System v2 (Invitrogen) according to the manufacturer’s protocol. PolyA+ RNA was isolated by two rounds of polyA-tailed selection using Dynabeads mRNA DIRECT Purification Kit (Invitrogen) according to the manufacturer’s protocol. To remove genomic DNA contamination, RNA was then treated with Turbo DNase and purified by Zymo-IC Column with RNA binding buffer.
50–100 ng ribo– or polyA+ RNA was fragmented by NEBNext Magnesium RNA Fragmentation Module at 94 °C for 4 min according to the manufacturer’s protocol and purified by Zymo-IC Column with RNA binding buffer. The fragmented RNA was mixed with 5 μl 10× T4 PNK reaction buffer (NEB), 5 μl T4 PNK (NEB), and 2.5 μl SUPERase.In RNase Inhibitor (Invitrogen) in a 50 µL final solution and incubated at 37 °C for 1 h. The 3’-repaired RNA was purified by Zymo-IC Column with RNA binding buffer and eluted with 10 μl nuclease-free H2O. The eluted RNA was then mixed with 1 μl synthetic 30mer spike-ins (2%) and 1 μl of 20 μM RNA adapter (5’-/5rApp/AGATCGGAAGAGCGTCGTG/3SpC3/-3’), incubated at 70 °C for 2 min and immediately placed on ice. Next, 2.5 μl 10× T4 RNA Ligase reaction buffer (NEB), 1 μl SUPERase.In RNase Inhibitor, 7.5 μl 50% PEG 8000 (NEB), and 2 μl T4 RNA Ligase 2, truncated KQ (NEB) were added to the mixture and the reaction was incubated at 25 °C for 2 h followed by 16 °C for 14 h. To digest excess adapters, the solution was further diluted to 47 μl with nuclease-free H2O and treated with 2 μl 5’-Deadenylase (NEB) at 30 °C for 1 h followed by adding 1 μl RecJf (NEB) and incubating at 37 °C for 1 h. The 3’-ligated RNA was purified by Zymo-IC Column with RNA binding buffer and eluted with 10 μl nuclease-free H2O. A 7 μl aliquot was subjected to BACS library construction, while the rest 3 μl was saved as control sample and diluted to 12.5 μl with nuclease-free H2O. For BACS, 1 M 2-bromoacrylamide (Enamine) was prepared by dissolving the solid in DMSO. 7 μl 3’-ligated RNA was added into a 20 μl solution containing 250 mM 2-bromoacrylamide and 625 mM phosphate buffer (pH 8.5) and incubated at 85 °C for 30 min. The treated RNA was double purified by Micro Bio-Spin P-6 Tris Column (Bio-Rad) and Zymo-IC Column with RNA binding buffer and finally eluted with 12.5 μl nuclease-free H2O. Both treated and control RNA samples were mixed with 1 μl of 2 μM RT primer (5’-ACACGACGCTCTTCCGATCT-3’) and 1 μl of 10 mM dNTP mix (NEB), incubated at 70 °C for 2 min and immediately placed on ice. Next, 4 μl 5× Maxima H– RT buffer (Thermo), 0.5 μl RiboLock RNase Inhibitor (Thermo), and 1 μl Maxima H– Reverse Transcriptase (Thermo) were added to the mixture and the reaction was incubated at 50 °C for 1 h. To digest excess RT primers, the solution was treated with 1 μl Exo I (NEB) and incubated at 37 °C for 30 min followed by adding 1 μl of 0.5 M EDTA (Sigma) to quench the reaction. To hydrolyze the RNA, 2.5 µl of 1 M NaOH (Sigma) was added and the solution was then incubated at 70 °C for 12 min followed by adding 2.5 µl of 1 M HCl (Sigma) to neutralize NaOH. The cDNA was finally purified with Dynabeads MyOne Silane (Invitrogen) and eluted with 13 µl nuclease-free H2O. The eluted cDNA was then mixed with 2 µl of 25 μM cDNA adapter (5’-/5Phos/NNNNNNAGATCGGAAGAGCACACGTCTG/3SpC3/-3’), incubated at 70 °C for 2 min and immediately placed on ice. Next, 5 μl 10× T4 RNA Ligase reaction buffer, 25 μl 50% PEG 8000, 0.5 μl of 100 mM ATP (NEB), 3.5 μl DMSO (Thermo), and 1 μl T4 RNA Ligase 1, high concentration (NEB) were added to the mixture and the reaction was incubated at 25 °C for 16 h. The ligated cDNA was purified with Dynabeads MyOne Silane and eluted with 15 µl nuclease-free H2O. The eluted DNA was amplified with NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) and NEBNext Ultra II Q5 Master Mix for 10 cycles according to the manufacturer’s protocol. The PCR products were purified with 0.8× AMPure XP beads and quantified with Qubit dsDNA HS Assay Kit (Thermo) according to the manufacturer’s protocol. BACS and control libraries were sequenced on NextSeq 2000 (60 bp paired end) with no PhiX added.

value: control


title: scRNA-seq_Ov3 PBMC of HGSOC patients


title: PBMC RNA, Elevated/Mid Blood Pressure, M9

value: Blood

value: Peripheral blood mono nuclear cells


title: DU145, enriched, scRNA

value: Prostate


title: N3-RT11-52

value: thoracic 11


title: scRNA-seq_Ov2 PBMC of HGSOC patients


title: PBMC RNA, Elevated/Mid Blood Pressure, M10


title: scRNA-seq_Ov1 PBMC of HGSOC patients


title: Huh7.5_ZIKA_control


title: scRNA-seq_Dn3 PBMC of healthy donors

description: Healthy control


title: Calu3_COVID_control


title: scRNA-seq_Dn2 PBMC of healthy donors

description: Healthy control


title: N3-RT11-51


title: Huh7.5_HCV_control


title: HepG2_HDV_BACS

value: bacs


title: PBMC RNA, Elevated/Mid Blood Pressure, M7


title: Huh7.5_HCV_BACS


title: PBMC RNA, Elevated/Mid Blood Pressure, M11


title: N3-RT11-50


title: N3-RT11-53


title: Calu3_COVID_BACS


title: N3-RT11-49


title: Elijah_control

value: Elijah


title: Elijah_BACS


title: PBMC RNA, Elevated/Mid Blood Pressure, M5


title: Raji_control

value: Raji


title: PBMC RNA, Elevated/Mid Blood Pressure, M4


title: Raji_BACS


title: C666.1_control_rep2


title: N3-RT11-47

value: hPropr


title: C666.1_control_rep1


title: C666.1_BACS_rep2


title: N3-RT11-48


title: PBMC RNA, High Blood Pressure, H27


title: PBMC RNA, Elevated/Mid Blood Pressure, M8


title: C666.1_BACS_rep1


title: PBMC RNA, Elevated/Mid Blood Pressure, M2


title: N3-RT11-45


title: Huh7.5_ZIKA_BACS


title: TRUB1_control_rep2

source_name: HeLa

value: HeLa


title: N3-RT11-44


title: TRUB1_control_rep3


title: PBMC RNA, Elevated/Mid Blood Pressure, M6


title: PBMC RNA, Elevated/Mid Blood Pressure, M1


title: TRUB1_control_rep1


title: PBMC RNA, Low Blood Pressure, N54


title: N3-RT11-43


title: TRUB1_BACS_rep3


title: TRUB1_BACS_rep2


title: PBMC RNA, Low Blood Pressure, N53


title: N3-RT11-42


title: PUS1_control_rep2


title: PBMC RNA, Elevated/Mid Blood Pressure, M3


title: PBMC RNA, Low Blood Pressure, N52


title: N3-RT11-41


title: PUS7_control_rep2


title: N3-RT11-46


title: PBMC RNA, Low Blood Pressure, N51


title: N3-RT11-40


title: PBMC RNA, Low Blood Pressure, N50


title: PUS7_control_rep1


title: PUS1_BACS_rep1


title: N3-RT11-39


title: PUS7_BACS_rep2


title: PBMC RNA, Low Blood Pressure, N49


title: N3-RT11-38


title: PUS7_BACS_rep1


title: IVT_BACS_rep1


title: N3-RT11-37


title: PBMC RNA, Low Blood Pressure, N48


title: TRUB1_BACS_rep1


title: HeLa_polyA+_control_rep1


title: PBMC RNA, Low Blood Pressure, N47


title: N3-RT11-36


title: HeLa_polyA+_BACS_rep1


title: PBMC RNA, Low Blood Pressure, N46


title: PUS1_control_rep1


title: HeLa_polyA+_BACS_rep2


title: HeLa_ribo–_control_rep4


title: N3-RT11-35


title: PBMC RNA, Low Blood Pressure, N45


title: PUS1_BACS_rep2


title: PBMC RNA, Low Blood Pressure, N44


title: HeLa_ribo–_BACS_rep4


title: HeLa_ribo–_control_rep3


title: N3-RT11-34


title: PBMC RNA, Low Blood Pressure, N43


title: HeLa_ribo–_BACS_rep3


title: IVT_BACS_rep2


title: HeLa_total_RNA_control_rep1


title: HeLa_total_RNA_control_rep2


title: N3-RT11-33


title: HeLa_total_RNA_BACS_rep1


title: HeLa_total_RNA_BACS_spike in_75%


title: PBMC RNA, Low Blood Pressure, N42


title: HeLa_polyA+_control_rep2


title: HeLa_total_RNA_BACS_rep2


title: N3-RT11-31


title: N3-RT11-32


title: PBMC RNA, Low Blood Pressure, N41


title: HeLa_total_RNA_BACS_spike in_50%


title: N3-RT11-30


title: HeLa_total_RNA_BACS_spike in_25%


title: PBMC RNA, Low Blood Pressure, N40


title: HeLa_total_RNA_BACS_spike in_0%


title: N3-RT11-29


title: PBMC RNA, Low Blood Pressure, N39


title: N3-RT11-28


title: PBMC RNA, Low Blood Pressure, N38


title: PBMC RNA, Low Blood Pressure, N37


title: N3-RT11-27


title: N3-RT11-26


title: PBMC RNA, Low Blood Pressure, N35


title: PBMC RNA, Low Blood Pressure, N34


title: N3-RT11-25


title: PBMC RNA, Low Blood Pressure, N36


title: N3-RT11-24


title: PBMC RNA, Low Blood Pressure, N33


title: N3-RT11-23


title: N3-RT11-22


title: N3-RT11-21


title: PBMC RNA, Low Blood Pressure, N31


title: PBMC RNA, Low Blood Pressure, N32


title: I520587-2

type: RNA

city: San Diego

first: Yanqing

last: Chen

address: 3210 Merryfield Row

institute: Johnson and Johnson

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Microarray processing was performed on GeneChip HT HG-U133+ PM 96-Array Plate on the Affymetrix Gene Titan MC instrument that automates array processing from target hybridization to data generation.

data_processing: All the raw data .CEL files that are associated with chips that are part of this study are uploaded to Affymetrix Expression console software for RMA normalization. Library files for the corresponding GeneChip HT HG-U133+ PM array are downloaded from the Affymetrix website. After normalization .CHP files are generated and these .CHP files represent the normalized data.

label: biotin

source_name: Skin biopsy

label_protocol: RNA samples were pooled from each extraction to create an aliquot for Amplification.  RNA from the pooled aliquot (40ng where available) were amplified using the Ovation Pico V2 automation kit.  RUCDR technical controls, RUCDR positive control and RUCDR negative control are used as controls on each plate.  Samples were processed on Caliper SciClone using the automated NuGEN Ovation Pico v2 protocol. cDNA QC is performed using the LabChipGX and cDNA is used as input in the fragmentation and labeling reaction that is performed using the NuGEN Encore Biotin Module designed specifically for fragmentation and labeling of cDNA for analysis on Affymetrix GeneChip® arrays.

extract_protocol: Using a disposable scalpel and forceps, the tissue samples were cut into fragments that weighed approximately 20 mg (± 2 mg).  For each tissue sample, a 20 mg (± 2 mg) tissue fragment was moved to a 2 mL Sarstedt tube and each received 400 µL of Buffer RLT Plus (containing 10 µL β-ME/1 mL of Buffer RLT Plus).  The tissue lysates were disrupted and homogenized using the TissueRuptor and disposable probes for 30 seconds. Each lysate was inspected and, if necessary, homogenized in additional increments of 30 seconds until uniformly homogeneous.  The homogenized RNA lysate was centrifuged at 7,000 RPM for 3 minutes and transferred to a new 2mL Sarstedt tube. RNA lysates were extracted using the Qiasymphony RNA Kit (Cat no. 931636), RNA FT 400 protocol, and eluted in 50 µL of RNFW. The RNA quantity and purity was assessed using the Trinean DropSense.  The RNA quality was assessed using the Caliper LabChip Gx.

treatment_protocol: RNA processing and extraction was performed by BioProcessing Solutions (BSA) according to their standard protocols. Specifically, prior to extraction, the tissue samples were thawed and RNALater solution was removed.

tag: study id

tag: subject id

value: Adalimumab

tag: time point

tag: skin

value: NL


title: I520587-1

tag: treatment

value: LS


title: I520589-1


title: 6502356122-01


title: 6501377146-01

value: Guselkumab


title: 6502456982-01

value: Placebo to Guselkumab


title: I520585-2


title: 6502283588-01


title: 6500742969-02


title: 6502356118-01


title: N3-RT11-20

tag: tissue

value: Dorsal root ganglia

value: Caucasian


title: 6502467568-01


title: 6500742968-01


title: 6502356120-01


title: 6500821468-01


title: 6500959295-01


title: N3-RT11-19

tag: donor id

value: Female


title: PBMC RNA, Low Blood Pressure, N30

value: Blood


title: PBMC RNA, Low Blood Pressure, N29

value: Peripheral blood mono nuclear cells


title: 6502356121-01


title: N3-RT11-18

tag: age(years)


title: I520586-1


title: 6500643761-01


title: PBMC RNA, Low Blood Pressure, N28


title: N3-RT11-17

tag: race


title: PBMC RNA, Low Blood Pressure, N27


title: N3-RT11-16

tag: gender


title: 6500591453-01


title: PBMC RNA, Low Blood Pressure, N26


title: 6500591452-01


title: 6500591454-01


title: N3-RT11-15

tag: region


title: PBMC RNA, Low Blood Pressure, N25


title: 6500591450-01


title: N3-RT11-13

tag: sequencing batch


title: PBMC RNA, Low Blood Pressure, N24


title: PBMC RNA, Low Blood Pressure, N23


title: 6500591445-02


title: 6500591445-01


title: 6500591448-01


title: N3-RT11-14

tag: dissected soma size


title: 6500550446-01


title: N3-RT11-12

tag: cell identity


title: PBMC RNA, Low Blood Pressure, N22

tag: cell type


title: 6500591455-01


title: 6500591442-02


title: 6500425711-02


title: 6500425710-02


title: 6500364972-10


title: 6500425710-01


title: 6500032409-02


title: N3-RT11-11


title: PBMC RNA, Low Blood Pressure, N21


title: 6500032407-01


title: 6500425709-02


title: N3-RT11-10


title: PBMC RNA, Low Blood Pressure, N20


title: N3-RT11-9


title: N3-RT11-8


title: 6500018016-01


title: 6500018014-02


title: N3-RT11-6


title: PBMC RNA, Low Blood Pressure, N19


title: N3-RT11-5


title: PBMC RNA, Low Blood Pressure, N16


title: 6500018032-02


title: 6202314539-01


title: 6202201689-01


title: N3-RT11-7


title: 6500018015-01


title: 6500018014-01


title: 6500018000-01


title: PBMC RNA, Low Blood Pressure, N15


title: N3-RT11-4


title: N3-RT11-3


title: 6201058400-01


title: 6201058402-01


title: PBMC RNA, Low Blood Pressure, N18


title: PBMC RNA, Low Blood Pressure, N13


title: PBMC RNA, Low Blood Pressure, N14


title: PBMC RNA, Low Blood Pressure, N17


title: N3-RT11-2


title: PBMC RNA, Low Blood Pressure, N12


title: 6201058401-01


title: 6500017931-02


title: 6200544433-01


title: 6200544427-01


title: 6200469030-01


title: 6201289568-01


title: N3-RT11-1


title: 6500017912-02


title: 6200422916-02


title: N3-RL2-92

value: lumbar 2


title: 6200422912-02


title: N3-RL2-91


title: PBMC RNA, Low Blood Pressure, N9


title: N3-RL2-90


title: PBMC RNA, Low Blood Pressure, N8


title: N3-RL2-88


title: 6200173767-02


title: PBMC RNA, Low Blood Pressure, N11


title: 6200421334-01


title: 6200268153-01


title: 6200173766-02


title: 6200469027-01


title: PBMC RNA, Low Blood Pressure, N10


title: N3-RL2-87


title: 6200022807-01


title: I520585-1


title: M077525-1


title: PBMC RNA, Low Blood Pressure, N6


title: PBMC RNA, Low Blood Pressure, N5


title: M077526-2


title: N3-RL2-85


title: N3-RL2-86


title: PBMC RNA, Low Blood Pressure, N4


title: I520369-1


title: N3-RL2-84


title: I520339-1


title: PBMC RNA, Low Blood Pressure, N7


title: PBMC RNA, Low Blood Pressure, N3


title: I520339-2


title: I520367-2


title: I520369-2


title: PBMC RNA, Low Blood Pressure, N2


title: H432377-1


title: I520338-1


title: PBMC RNA, Low Blood Pressure, N1


title: 6200022807-02


title: N3-RL2-80


title: H432376-2


title: N3-RL2-83


title: N3-RL2-82


title: N3-RL2-78


title: Mdd01_RNAseq

city: Qingdao

first: Jun-Jie

state: Shandong

address: Changcheng 700

department: Qingdao Agricultural University

country: China

institute: College of Life Sciences

data_processing:
AASRA software for reference genome alignment.
SPORTS1.0 pipeline for small RNA annotation.
miRNA prediction: miRDeep2 and miRA; piRNA prediction: Piano; siRNA prediction.
The expression levels of miRNAs is normalized by TPM fuction.
Differential small RNA screening: DESeq2
Assembly: mm9
Supplementary files format and content: The tab-delimited text file includes small RNA reads for each sample.
Supplementary files format and content: The tab-delimited text file includes annotation result of small RNA for each sample.

organism: Mus musculus

source_name: Testis

extract_protocol:
Total RNA was extracted from sperm using the TRIzol reagent and reversed into cDNA.
The 18-40 nt sncRNAs isolated from total RNAs were used for small RNA-seq. The conduction, preparation, and quality examination of small RNA libraries were performed by the MGIEasy Small RNA Library Prep Kit (MGI, Shenzhen, China).

treatment_protocol: Mice were exposed to different stressors at random every day, including an empty cage, a 45° cage tilt, a damp sawdust cage, white noise, strobe light, restraint in a plastic tube, social isolation, and circadian disturbance. The mice in the control group were undisturbed except for feeding and cage cleaning.

value: Testis

tag: strain

value: Testicular cells

value: Mdd


title: N3-RL2-77


title: Ctrl02_RNAseq

value: control


title: I520367-1


title: N3-RL2-76


title: 6502456983-01


title: Ctrl01_RNAseq


title: 6502456981-01


title: 6503034570-01


title: 6503034569-01


title: H432376-1


title: 6502356117-01


title: 6502283589-01


title: 6502296779-01


title: Mdd02_RNAseq


title: 6502456984-01


title: N3-RL2-79


title: H432377-2


title: HCT_C3

city: Sharjah

first: Rifat

last: Hamoudi

state: Sharjah

address: M32 Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, , Sharjah

department: Clinical Sciences

country: United Arab Emirates

institute: University of Sharjah

data_processing:
RNA-seq data analysis was performed using the Ion Torrent Software Suite version 5.4. In order to align the raw sequencing reads generated by Ion Torrent sequencing against the reference sequence from the hg19 (GRCh37) assembly, the Torrent Map-ping Alignment Program (TMAP) was utilized, and the specificity and sensitivity were maintained by implementing a two-stage mapping approach by employing BWA-short, BWA-long, SSAHA, Super-maximal Exact Matching [18] and the Smith-Waterman algorithm for optimal mapping. The raw read counts of the tar-geted genes were normalized using the Fragments Per Kilobase Million (FPKM) nor-malization method. Principal component analysis (PCA) was applied to the samples using the R statistical software (version 4.2.0). Differentially expressed gene (DEG) analysis was performed using the DESeq2 R/Bioconductor package with raw read counts from the RNA sequencing data to identify the differentially expressed genes (DEGs) in each comparison of cell lines with CARD11 transfected against cell lines with empty vector transfected as well as of the patients with low (CARD11-) and high (CARD11+) CARD11 expressions. Among 10 adenoma patients, four samples were identified as having low CARD11 expression (CARD11-), and six samples were identified as having high CARD11 expression (CARD11+), whereas in 13 carcinoma samples, eight samples were identified as having low CARD11 expression (CARD11-) and five samples were identified as having high CARD11 expression (CARD11+).
Assembly: GRCh37 (hg19)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Following transfection, transfected and non-transfected cells were collected by trypsinization. Cells were pelleted and RNA was extracted from the cell pellet using the Qiagen RNeasy kit according to the manufacturer’s instructions. Three sequential (3 µm) sections of the FFPE tissue biopsies from the adenoma and carcinoma cases were subjected to RNA extraction using Recover All kit according to the manufacturer’s instructions. Genomic DNA removal from all RNA extractions was ensured by treating the RNA with TURBO DNAase-free TM Kit.
A total of 50 and 30 ng of extracted and Turbo DNase treated RNAs proceeded for whole transcriptome sequencing using a targeted AmpliSeq Transcriptome panel which is designed to target over 21,000 specific human RNA transcripts using a high-throughput multiplexed method on Ion S5 XL Semiconductor sequencer using the Ion 540-Chip. In brief, total RNAs were first processed with SuperScript VILO cDNA synthesis kit and the resulting cDNAs were amplified using Ion AmpliSeq™ transcriptome human gene expression kit to prepare the libraries. The prepared libraries were purified using Agencourt AMPure XP Beads and the purified libraries were quantified using an Ion Library TaqMan™ Quantitation Kit. The libraries were diluted to ~100 pM and pooled by combining an equal volume of each barcoded library, then proceeded amplification using emulsion PCR on Ion OneTouch™ 2 instrument, and enriched on Ion OneTouch™ ES as per the manufacturer’s instructions. Thus, prepared template libraries were then sequenced with Ion S5 XL Semiconductor sequencer using the Ion 540™ Chip.

tag: cell line

value: CRC cell line

tag: genotype

value: KRAS mutant

value: Transfection with empty vector


title: N3-RL2-72

value: hPropr


title: 6501377147-01

tag: study id

tag: subject id

value: LS


title: HCT_C2


title: 6500948035-01

value: Guselkumab

tag: time point

tag: skin


title: 6502416760-01

tag: treatment

value: Adalimumab


title: HCT_T3

value: Transfection with CARD11 plasmid


title: HT_T3

value: p53 mutant


title: 6500779545-01

value: Placebo to Guselkumab


title: 6500948031-01


title: 6502283587-01


title: 6500948034-01


title: N3-RL2-75

tag: tissue

value: Dorsal root ganglia

tag: donor id

value: Caucasian

value: Female


title: HCT_T2


title: N3-RL2-69

tag: age(years)

tag: race

value: lumbar 2


title: HT_T2


title: N3-RL2-68

tag: gender

tag: region


title: 6500959297-01


title: N3-RL2-74

tag: sequencing batch

tag: dissected soma size


title: 6500959296-01


title: 6500591451-01


title: HCT_T1

tag: cell type


title: HT_T1


title: 6500591442-01


title: 6500550443-01


title: N3-RL2-73

tag: cell identity


title: HT_C3

tag: cell line


title: 6500550444-01


title: 6501377149-01


title: N3-RL2-71


title: 6500550442-01


title: N3-RL2-65


title: 6500948033-01


title: 6500550441-01


title: HCT_C1

tag: genotype


title: 6500742969-01

tag: study id


title: N3-RL2-64


title: N3-RL2-70


title: 6500550440-01

tag: subject id


title: 6500779543-01

tag: time point


title: 6500689380-01

tag: skin


title: 6500550437-01

tag: treatment


title: CA2_2_CARD11_NEG3

description: Carcinoma.txt

source_name: Carcinoma

tag: tissue

value: Carcinoma

tag: card11 level

value: low

value: Invasive adenocarcinoma


title: N3-RL2-63

tag: donor id

tag: age(years)


title: N3-RL2-67

tag: race

tag: gender


title: N3-RL2-62

tag: region

tag: sequencing batch


title: N3-RL2-66

tag: dissected soma size


title: 6500550436-01


title: CA2_2_CARD11_POS3

description: Carcinoma.txt

value: high


title: 6500643760-01


title: 6500550435-01


title: 6500550433-02

value: NL


title: N3-RL2-61

tag: cell identity


title: 6500591449-01


title: HT_C2

tag: cell line

tag: cell type

value: CRC cell line

value: Transfection with empty vector


title: HT_C1

tag: genotype


title: 6500550438-01

tag: study id

tag: subject id

value: LS


title: N3-RL2-60


title: 6500425711-01

value: Guselkumab

tag: time point

tag: skin


title: CA2_2_CARD11_NEG1

description: Carcinoma.txt

tag: tissue

tag: treatment


title: N3-RL2-58

tag: donor id


title: CA_1_CARD11_NEG5

description: Carcinoma.txt

tag: card11 level


title: N3-RL2-57

tag: age(years)

tag: race


title: 6500514429-02


title: 6500304313-01


title: 6500550433-01


title: 6500304315-01


title: N3-RL2-56

tag: gender

tag: region


title: 6500304314-01

value: Adalimumab


title: CA2_2_CARD11_NEG2

description: Carcinoma.txt


title: CA2_2_CARD11_POS2

description: Carcinoma.txt


title: 6500514429-01


title: 6500444967-01


title: 6500444965-01


title: 6500032409-01


title: N3-RL2-59

tag: sequencing batch

tag: dissected soma size


title: CA2_2_CARD11_POS1

description: Carcinoma.txt


title: CA_1_CARD11_NEG3

description: Carcinoma.txt


title: 6500425709-01


title: 6500032408-02


title: N3-RL2-54

tag: cell identity


title: CA_1_CARD11_NEG4

description: Carcinoma.txt


title: CA_1_CARD11_POS2

description: Carcinoma.txt


title: N3-RL2-55


title: N3-RL2-52


title: 6500032410-01


title: CA_1_CARD11_NEG2

description: Carcinoma.txt


title: 6500032410-02


title: CA_1_CARD11_POS1

description: Carcinoma.txt


title: N3-RL2-53


title: CA_1_CARD11_NEG1

description: Carcinoma.txt


title: AD_CARD11_NEG4

description: Adenoma.txt

source_name: Adenoma

value: Adenoma

value: Tubular adenomas


title: N3-RL2-50


title: AD_CARD11_NEG3

description: Adenoma.txt


title: 6500018051-02


title: 6500018051-01


title: N3-RL2-49


title: 6500032408-01


title: 6500018050-01


title: AD_CARD11_NEG2

description: Adenoma.txt


title: 6500017929-01


title: 6500018032-01

value: Placebo to Guselkumab


title: 6500018050-02


title: 6500017931-01


title: 6500017997-01


title: 6500017912-01


title: 6500018034-01


title: 6202384147-01


title: 6202384144-01


title: N3-RL2-51

value: Dorsal root ganglia


title: 6202363489-01


title: N3-RL2-48

value: Caucasian


title: AD_CARD11_NEG1

description: Adenoma.txt


title: AD_CARD11_POS6

description: Adenoma.txt


title: 6500017999-01


title: N3-RL2-47

value: Female


title: N3-RL2-46

value: lumbar 2


title: N3-RL2-45


title: AD_CARD11_POS4

description: Adenoma.txt


title: 6202090235-01


title: 6202314538-01


title: AD_CARD11_POS5

description: Adenoma.txt


title: 6200642972-01


title: 6202384148-01


title: AD_CARD11_POS3

description: Adenoma.txt


title: 6201125891-01


title: N3-RL2-43


title: 6201125887-01


title: AD_CARD11_POS2

description: Adenoma.txt


title: 6200623967-01


title: N3-RL2-42


title: N3-RL2-41


title: AD_CARD11_POS1

description: Adenoma.txt


title: EC-HC-3d

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description: 10x Genomics

data_processing:
Sequencing was done on Nextseq2000 and raw reads were aligned against the zebrafish genome (DanRer11) and counted by StarSolo
Preprocessed counts were further analysed using Scanpy ollowed by secondary analysis in Annotated Data Format.
Preprocessed counts were further analyzed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 5 cells in total that did not express more than 300 genes or had a mitochondrial content greater than 5%. Furthermore, we filtered 24259 genes if they were detected in less than 30 cells (<0.01%).
Raw counts per cell were normalized to the median count over all cells and transformed into log space to stabilize variance. We initially reduced dimensionality of the dataset using PCA, retaining 50 principal components. Subsequent steps, like low-dimensional UMAP embedding (McInnes & Healy, https://arxiv.org/abs/1802.03426) and cell clustering via community detection, were based on the initial PCA.
Final data visualization was done by scanpy and cellxgene packages.
Assembly: danRer11
Supplementary files format and content: starsolo outputs

organism: Danio rerio

source_name: Heart

growth_protocol: Embryos/larvae were grown in 28-degree incubator until extraction at 48 or 72 hours post fertilization.

extract_protocol:
Embryos were raised in a solution composed of 0.33 Danieau's medium, containing the following concentrations: 17.4 mM NaCl, 0.21 mM KCl, 0.12 mM MgSO4·H2O, and 0.18 mM Ca(NO3)2, while being maintained at a stable temperature of 28°C. To isolate EdCs for the single-cell RNA sequencing experiment, hearts from 48- and 72-hpf Tg(kdrl:nls-mCherry); Tg(cd41:GFP) larvae were manually dissected in DMEM + 10% FBS.   Hearts were then centrifuged for 60 seconds at 3000 rpm, washed with 1 mL Hanks’ Balanced Salt Solution and dissociated into single cells by incubating in 100 μl Enzyme 1 and 5 μl Enzyme 2 (Pierce Cardiomyocyte Dissociation Kit, Thermo Fisher Scientific, Cat#88281) for 20 minutes at 300 rpm in a 30°C shaker 79.  The samples were centrifuged for 5 minutes at 3000 rpm, the supernatant was discarded, and fresh medium was added to the dissociated cells and passed through 40 μM-filter polystyrene 5ml tubes.  Negative controls of non-fluorescent hearts or single-color fluorescent hearts were prepared to define the sorting gates.  Cells were sorted using the BD FACSAria™ III (BD Biosciences) instrument.   Live cells were selected by exclusion of DAPI using 30mW 405nm excitation paired with 450/50 nm band pass filter.  The software used for sorting and analysis is BD FACSDiva v8.0.1.  Single positive Tg(kdrl:nls-mCherry)+ cells and double-positive Tg(kdrl:nls-mCherry)+; Tg(cd41:GFP)+ cells were sorted and collected into tubes with DMEM + 10% FBS.  Cells from both collected samples were immediately combined and processed for the single-cell RNA sequencing.  mCherry fluorescence was measured with 50mW 561nm excitation paired with 610/20nm band pass filter. GFP fluorescence was measured with 50mW 488nm excitation paired with 530/30 band pass filter. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer’s protocol to obtain 4.000 (2d-HC) and 8.000 (3d, 10.497 EC, 1.569 HC) single cell data points per sample, respectively. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10xGenomics).
Library preparation was conducted according to the manufacturer indications.

value: Heart

tag: cell type

value: Endocardial cells

value: Tg(kdrl:nls-mCherry); Tg(cd41:GFP)

tag: developmental stage

value: 72 hours post fertilization


title: 6200544440-01

tag: study id


title: N3-RL2-40


title: 6200544439-01

tag: subject id


title: 6200623966-01

tag: time point


title: 6201289570-01

tag: skin


title: EC-2d

description: 10x Genomics

tag: tissue

tag: genotype

value: 48 hours post fertilization


title: 6200544423-01

tag: treatment


title: 6200544432-01


title: 6200544437-01


title: 6200544438-01


title: 6200469029-01


title: 6200469031-01


title: N3-RL2-39

tag: donor id


title: 6200422915-01


title: N3-RL2-38

tag: age(years)


title: HFSC, EGFRDEgr2, 3

city: Vienna

first: Thomas

last: Bauer

state: Vienna

address: Borschkegasse 8A

department: Center for Cancer Research

country: Austria

institute: Medical University of Vienna

data_processing:
The kallisto pipeline was used to quantify the counts from the raw sequencing data.
Assembly: mm10
Supplementary files format and content: excel file includes estimated counts matrix for each sample

source_name: skin

extract_protocol:
Viable CD45-CD34+Sca-I- cells were sorted from epidermal single cell suspensions of 1-month-old EGFRΔEgr2 (n=3) and littermate controls (n=3) into Trizol LS Reagent (Thermo Fisher Scientific) using a FACS Aria III. RNA was extracted with the column-based miRNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol. cDNA synthesis was performed with Superscript IV Reverse Transcriptase (Thermo Fisher Scientific).
Samples were sent to Novogene, UK for quality control, library preparation and sequencing using Novaseq 6000 PE150.

value: skin

tag: age

value: 1 month

value: hair follicle stem cells

value: Egfr-floxed Egr2-Cre


title: Epidermis, Egfr-floxed Egr2-Cre, 4 reps pooled, scRNA-seq

description:
KO 3M
10X Genomics

data_processing:
The CellRanger pipeline version 7.0.0 was used to process raw sequencing files and produce feature-barcode matrices.
Assembly: mm10
Supplementary files format and content: CellRanger output files of raw and filtered (only cellular) barcodes.

source_name: Epidermis

extract_protocol:
12.000 viable CD45-Sca-I- cells and 12.000 viable CD45+ were sorted from pooled epidermal single cell suspensions of 3-month-old EGFRΔEgr2 (n=4) into a 0.04% BSA solution using a BD FACSMelody™ Cell Sorter (Biosciences).
Single-cell cDNA libraries were generated using the droplet-based Chromium Next GEM Single Cell 5’ Kit v2 (Cat.nr. 1000265, 10x Genomics) following manufacturer’s instructions. Libraries were sequenced on insert machine name.

value: Epidermis

value: 3 months

value: immune cells and hair follicle cells

tag: strain


title: N3-RL2-37

tag: race

tag: gender

tag: region


title: HFSC, EGFRDEgr2, 1


title: N3-RL2-36

tag: sequencing batch

tag: dissected soma size

tag: cell identity


title: 6200422912-01

tag: study id

value: Adalimumab

value: LS


title: 6200268154-01

tag: subject id

value: Guselkumab


title: 6200422916-01

tag: time point


title: 6200173770-01

tag: skin


title: 6200173770-02

value: NL


title: 6200173769-01


title: 6200173768-02


title: 6200173768-01


title: N3-RL2-34

tag: tissue

value: Dorsal root ganglia

value: Caucasian

value: Female

value: lumbar 2


title: HFSC, WT, 2

tag: cell type

tag: genotype

value: wildtype


title: N3-RL2-33

tag: donor id


title: HFSC, WT, 3


title: HFSC, EGFRDEgr2, 2


title: 6200173767-01

tag: treatment

value: Placebo to Guselkumab


title: N3-RL2-32

tag: age(years)


title: N3-RL2-35


title: 6200022808-01


title: HFSC, WT, 1

value: skin

tag: age


title: N3-RL2-30

tag: race


title: WT-3

city: Wuhan

first: ZHIYI

last: CHEN

address: WuHan

institute: WuHan University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt (minimum read length:40,quality-cutoff 20)
rRNA was removed by bowtie2
Trimmed sequence reads were mapped to mm39 using STAR
Read count extraction were performed using featureCount
Assembly: mm39
Supplementary files format and content: count maritx for nine samples

source_name: testis

extract_protocol:
Total RNA was used as input material for the RNA sample preparations.
Enriching mRNA using mRNA Capture Beads (oligo dT magnetic beads).
Sequencing libraries were generated.

value: testis

value: wild type


title: WT-1


title: WT-2


title: N3-RL2-29

tag: gender


title: 6200022809-02


title: 6200022808-02


title: 6200022806-01


title: N3-RL2-28

tag: region


title: 6200022791-01


title: 6200022741-02


title: 6200022739-02


title: 6200022791-02


title: 6200022806-02


title: 6200022809-01


title: 6200022789-02


title: 6200022789-01


title: N3-RL2-31

tag: sequencing batch


title: N3-RL2-27

tag: dissected soma size


title: GM1142KO-2

value: knock out


title: GM1142KO-3


title: GM1142KO-1


title: 6200022741-01


title: N3-RL2-26

tag: cell identity


title: GM4779-GM1142-DKO-1


title: Pca_00587

city: Seoul

first: BYULA

last: JEE

address: 81 Irwon-Ro Gangnam-gu

department: Urology

country: South Korea

institute: Samsung medical center

data_processing:
The reads were mapped to the GRCh38 human reference genome using STAR (version 2.5.2b) with default parameter.
The counts of reads mapping to each gene were calculated using RSEM (version 1.3.0) with default parameter.
Assembly: GRCh38

source_name: Prostate cancer

extract_protocol:
Total RNA was extracted utilizing the RNA extraction kit (Rneasy Mini Kit, QIAGEN), and RNA integrity was verified using a 2100 Bioanalyzer (Aglient).
The libraries for sequencing were generated using the QuantSeq 3’ Library Prep Kit (Lex-ogen Inc., Vienna, Austria) according to the manufacturer’s instructions

value: Prostate cancer

tag: disease state

value: Tumor

tag: cluster subtype


title: N3-RL2-25


title: Pca_00584


title: GM4779-GM1142-DKO-2


title: N3-RL2-24


title: Pca_00452

value: Normal


title: GM4779-GM1142-DKO-3


title: Pca_00450


title: heart_sleep fragmented_5 weeks_Control 3

city: Beijing

first: Ling

last: Zhong

address: Wangfujing Street

department: Department of Endocrinology

institute: Peking Union Medical College Hospital

description: gene expression after 5 weeks of sleep fragmentation

hyb_protocol: Then the RNA was hybridized using an Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242).

scan_protocol: Following microarray hybridization and washing, the processed slides were scanned with an Agilent DNA microarray scanner (Agilent p/n G2565BA).

data_processing: The raw gene expression data were extracted from Agilent Feature Extraction Software (Version 10.5.1.1) and imported into Agilent GeneSpring GX software (version 11.0) for further analysis. The microarray data sets were normalized in GeneSpring GX using the Agilent Feature Extraction one-color scenario (primarily using quantile normalization).

source_name: heart, sleep fragmented, 5 weeks, Control 3

label_protocol: The RNA was amplified and labeled using the Agilent Quick Amp One-Color labeling kit (Agilent p/n 5190-0442).

extract_protocol: Total RNA was isolated from the heart using Total RNA Extraction Reagent (Invitrogen, Bio-Tek, Inc., USA). The RNA was further purified using RNeasy spin columns (Qiagen p/n 74104) according to the manufacturer's instructions.

treatment_protocol: The ventricles were isolated from mice after intervention.

value: heart

value: female

value: 21 weeks


title: heart_sleep fragmented_5 weeks_Control 2

source_name: heart, sleep fragmented, 5 weeks, Control 2


title: heart_sleep fragmented_5 weeks_Control 1

source_name: heart, sleep fragmented, 5 weeks, Control 1


title: heart_sleep fragmented_5 weeks_SF 3

source_name: heart, sleep fragmented, 5 weeks, SF 3


title: heart_sleep fragmented_5 weeks_SF 2

source_name: heart, sleep fragmented, 5 weeks, SF 2


title: 6200022739-01

tag: study id

tag: subject id

tag: time point

value: LS


title: ko9

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

data_processing:
Sequence reads were mapped and genes counted using STAR 2.5.0a to GRCm39/Ensembl 104
Assembly: GRCm39
Supplementary files format and content: Raw read count in tab-delimited format

source_name: Liver

extract_protocol:
Total RNAs was extracted from the mouse livers with RNeasy kit (QIAGEN)
stranded mRNA libraries were constructed by using Novogene NGS Stranded RNA Library Prep Set (PT044). The library was validated with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection

treatment_protocol: 8 weeks western diet

tag: tissue

value: Liver

tag: strain


title: heart_sleep fragmented_5 weeks_SF 1

source_name: heart, sleep fragmented, 5 weeks, SF 1


title: Pca_00449


title: N3-RL2-21

source_name: Dorsal root ganglia

value: Dorsal root ganglia

tag: donor id

value: Caucasian


title: ko7

tag: genotype


title: Chondrocytes, untreated, H12, normoxia, R3

city: Paris

first: Augustin

last: Latourte

address: Hôpital Lariboisière

country: France

institute: Université Paris Cité

data_processing:
Reads were aligned to the mouse genome (mm10) with Tophat2, then reads were counted with HTSeq. The DESeq2 package was used for analysis of differential gene expression, and Benjamini-Hochberg adjusted p values were calculated to adjust for multiple testing.
Assembly: mm10
Supplementary files format and content: xlsx (matrix table), raw counts

source_name: cartilage

growth_protocol: Mouse primary chondrocytes were cultured with 21% (normoxia) or 1% (hypoxia) oxygen in 10% FCS DMEM as described

extract_protocol:
Total RNA was isolated by using TRIzol reagent (Life Technologies) and further purified (RNeasy Mini kit, Qiagen). At each step, RNA was checked on a bioanalyzer (RNA 6000 Pico Kit, Agilent) and quantified on Qubit. Purification was performed with the Ribo-Zero Magnetic Gold kit (Tebu Bio) to remove ribosomal RNA, followed by another purification with the RNeasy MinElute Cleanup Kit (Qiagen).
cDNA libraries were constructed by using the TruSeq RNA Sample Prep kit (Illumina).
Three barcoded cDNA libraries were made for each condition, at each time point.

treatment_protocol: Chondrocytes were then stimulated or not with IL-6 or IL-6R (100 ng/ml each) for 12 hr in serum-free DMEM.

value: cartilage

tag: cell line

value: primary

tag: cell type

value: chondroyte

tag: treatment

value: no


title: ko8


title: N3-RL2-22

tag: age(years)

tag: race

tag: gender

value: Female

value: lumbar 2


title: Chondrocytes, treated, H12, hypoxia, R3

value: wild type


title: Pca_00447

value: Prostate cancer


title: Chondrocytes, untreated, H12, hypoxia, R3


title: N3-RL2-20

tag: region

tag: sequencing batch

tag: dissected soma size


title: Chondrocytes, treated, H12, normoxia, R3


title: Chondrocytes, untreated, H0, normoxia, R3


title: Pca_00212

tag: disease state


title: Pca_00211

value: Tumor

tag: cluster subtype


title: ko5


title: ko6


title: Chondrocytes, untreated, H0, hypoxia, R3


title: N3-RL2-19

tag: cell identity


title: N3-RL2-23


title: Pca_00164

value: Normal


title: Chondrocytes, treated, H12, normoxia, R2


title: ko4


title: Pca_00163


title: N3-RL2-17


title: N3-RL2-44


title: Pca_00162


title: ko3


title: N3-RL2-16


title: Chondrocytes, treated, H12, hypoxia, R2


title: Chondrocytes, untreated, H12, normoxia, R2


title: Pca_00161


title: ko34


title: N3-RL2-15


title: ko33


title: N3-RL2-14


title: Pca_00160


title: Chondrocytes, untreated, H12, hypoxia, R2


title: Chondrocytes, untreated, H0, normoxia, R2


title: N3-RL2-13


title: ko32


title: Pca_00078


title: Chondrocytes, untreated, H0, hypoxia, R2


title: ko31


title: ko30


title: N3-RL2-12


title: Chondrocytes, treated, H12, normoxia, R1


title: N3-RL2-18


title: Pca_00074


title: N3-RL2-11


title: Pca_00073


title: N3-RL2-10


title: ko2


title: N3-RL2-9


title: ko27


title: Pca_00071


title: ko26


title: Pca_00070


title: Pca_00067


title: Pca_00069


title: Pca_00075


title: Chondrocytes, untreated, H0, hypoxia, R1


title: Pca_00066


title: ko20


title: ko22


title: Pca_00065


title: Chondrocytes, treated, H12, hypoxia, R1


title: Chondrocytes, untreated, H12, normoxia, R1


title: N3-RL2-4


title: N3-RL2-8


title: ko17


title: Pca_00064


title: N3-RL2-3


title: Pca_00063


title: N3-RL2-6


title: ko15


title: Pca_00062


title: N3-RL2-5


title: N3-RL2-1


title: ko1


title: N2-RT12-96

value: thoracic 12


title: ko14


title: Pca_00061


title: Chondrocytes, untreated, H0, normoxia, R1


title: Chondrocytes, untreated, H12, hypoxia, R1


title: ko23


title: Pca_00060


title: N2-RT12-95


title: ko11


title: N3-RL2-2


title: dn9


title: Pca_00059


title: N3-RL2-7


title: ko16


title: N2-RT12-94


title: dn8


title: N2-RT12-93


title: Pca_00058


title: Pca_00056


title: N2-RT12-92


title: dn7


title: Pca_00055


title: dn5


title: N2-RT12-91


title: N2-RT12-90


title: Pca_00054


title: dn4


title: Pca_00053


title: N2-RT12-89


title: dn33


title: dn34


title: N2-RT12-87


title: N2-RT12-88


title: dn31


title: Pca_00051


title: dn2


title: Pca_00052


title: dn29


title: Pca_00049


title: N2-RT12-85


title: N2-RT12-86


title: Pca_00048


title: VYS_MEHP_pos (551958A03)

type: genomic

city: East Lansing

first: Karilyn

middle: E

last: Sant

state: MI

address: 1355 Bogue St., Life Science B440

department: Pharmacology & Toxicology

institute: Michigan State University

description: MBD-cap enriched fractions were labeled with Cy5; control fractions were labeled with Cy3

hyb_protocol: Both labeled fractions were pooled for each sample, and allowed to hybridize for 20 h to a NimbleGen Mouse DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Arrays (Roche).

scan_protocol: Arrays were washed and then scanned in the Glover laboratory in the University of Michigan Department of Human Genetics using the NimbleGen MS 200 Microarray Scanner (Roche).

data_processing:
Microarray images were obtained and analyzed using the NimbleGen DEVA Software v2.3 (Roche). Raw Cy5 and Cy3 signal intensities for each aligned and analyzed array were exported for analysis on the log2 scale.
Within-array normalization of the raw data was performed using LOESS on each array using the Limma package in R 2.4.1.

source_name: MBD-cap enriched genomic DNA samples from MEHP-treated, NTD+ mouse visceral yolk sacs

label_protocol: Methyl-CpG binding domain-based capture (MBD-cap) was utilized to enrich the methylated fractions of each sample, using the protocols outlined by the Methylated DNA Enrichment Kit (Epimark). Whole genome amplification of the methylation-enriched samples was performed by using the GenomePlex Complete Whole Genome Amplification Kit (Sigma). These methylation-rich samples were labeled with Cy5 cyanine dye and the control fractions were labeled with Cy3 cyanine dye, using the NimbleGen Dual-Color DNA Labeling Kit (Roche).

extract_protocol: Genomic DNA was extracted from each samples using a phenol-chloroform extraction method, and each sample was divided into two aliquots and sheared to 200-1000 bp fragment sizes using sonication (Episonic).

value: visceral yolk sac

tag: exposure

value: mono-2-ethylhexyl phthalate (MEHP) (100ug/ml)

tag: neural tube defect status

value: positive

tag: sample type

value: MBD-cap enriched fraction

source_name: control fraction

value: control fraction


title: dn28

tag: tissue

value: Liver

tag: strain


title: N2-RT12-84

data_processing:
Raw sequencing data was demultiplexed with bcl2fastq2 v.2.20 (Illumina)
Demultiplexed data was trimmed with Cutadapt to remove Tn5 transposon adapter sequences.
The trimmed data were aligned to human genome using STAR v.2.7.9a49.
STAR quantMode GeneCounts was used to quantify unique mapped reads to gene counts.
Gene counts file was used for the downstream analysis
Assembly: human genome (GRCh38 GENCODE as the reference genome, and GRCh38.104. GTF as the annotation)
Supplementary files format and content: Comma-separated file includes raw counts for each Sample

extract_protocol:
Human DRG tissues were procured from National Disease Research Interchange (NDRI). The research application was approved by the NDRI Feasibility Committee (RLUW1 01). Six DRGs between T11 to L5 of three human donors aged from 23- 61 years were used in this study. The dissected DRG tissues from human donors were immediately imbedded in OCT, shipped to the Luo lab on dry ice and stored in -80 ℃ until use. The information of DRGs and dis-identified donors and screening criteria are summarized in the manuscript Supplementary Tables 1 & 2. The hDRGs imbedded in OCT were cryosectioned (Cryostat Leica Cm1950) into 20 μm sec-tions and mounted onto Arcturus PEN Membrane Frame Slides (Applied biosystems, LCM0521). One of every five consecutive sections was collected for laser capture microdissec-tion to avoid repeated dissection of the soma from the same neuron in different sections. The slides were stored in -80 ℃ until further use.On the day of laser capture microdissection, the slides were transferred to the SBDRC laser capture microdissection (LCM) core on dry ice. Before dissection, the section was briefly stained with RNase free Arcturus™ Histogene™ staining solution (Applied biosystems, 12241-05) for better visualization of neuronal soma: 70% cold EtOH for 30s; Histogene™ staining for 10s; 70% cold EtOH for 30s; 95% cold EtOH for 30s; 100% cold EtOH for 30s and air dry for 2min. Then, the slide was put onto laser capture microdissection microscope system (Leica LMD6) for the neuronal soma dissection. The laser was calibrated, and the laser intensity was adjusted to achieve best dissection efficiency. The dissected individual neuronal soma was col-lected in the cap of a 200 μl PCR tube containing 4 μl lysis buffer.
The sequencing library was generated following Smart-seq2 workflow. The libraries passing through all quality con-trols were selected for the final sequencing.

value: Dorsal root ganglia

tag: donor id

value: Caucasian


title: Pca_00046


title: dn22

tag: genotype


title: VYS_MEHP_pos (551959A03)


title: N2-RT12-83


title: dn21


title: N2-RT12-82


title: Pca_00045


title: EMB_CTL_neg (551958A02)

source_name: MBD-cap enriched genomic DNA samples from DMSO-treated (control), NTD- mouse embryos

value: whole embryos

value: dimethyl sulfoxide (DMSO) (control) (0.01% v/v)

value: negative


title: MDA-MB-231_TCI04 treated_rep3

city: Tianjin

first: Ping

last: Zhou

state: Tianjin

address: No1 Huanhuxi Load

institute: Tianjin Medical University Cancer Institute and Hospotal

description: Gene expression data from 50 μM TCI04 treated MDA-MB-231 cells

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: MDA-MB-231, 50 μM TCI04 treated, 48h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MDA-MB-231 cells were cultured in DMEM with 10% FBS.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: MDA-MB-231 cells were treated with 50 μM of TCI04 or PBS for 48 h.

tag: cell line

value: MDA-MB-231 cell line

tag: agent


title: N2-RT12-81

tag: age(years)

tag: race

value: Female


title: dn20


title: Pca_00044

value: Prostate cancer


title: Pca_00050

value: Tumor


title: Pca_00043


title: dn1


title: N2-RT12-80

tag: gender

tag: region


title: EMB_MEHP_neg (551960A02)

source_name: MBD-cap enriched genomic DNA samples from MEHP-treated, NTD- mouse embryos


title: MDA-MB-231_TCI04 treated_rep1


title: N2-RT12-79

tag: sequencing batch

tag: dissected soma size


title: MDA-MB-231_Ctrl_rep3

description: Gene expression data from PBS treated MDA-MB-231 cells

source_name: MDA-MB-231, PBS treated, 48h

value: PBS


title: MDA-MB-231_TCI04 treated_rep2


title: dn19


title: dn18


title: MDA-MB-231_Ctrl_rep2


title: Pca_00041

tag: disease state

tag: cluster subtype


title: EMB_MEHP_neg (551962A03)

tag: exposure


title: ChIP-seq on AP2-LT in a AP2-LT+3xHA 3D7 parasite line at 40hpi replicate 3 IP

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

library_source: genomic

data_processing:
Fastq files were trimmed for low quality reads and adator sequence removal using Trimmomatic (v 0.38.0). Single-end options were "SE ILLUMINACLIP:TrueSeq3-SE:2:30:10 SLIDINGWINDOW:4:30". Paired-end options were "PE ILLUMINACLIP:TrueSeq3-PE:2:30:10 SLIDINGWINDOW:4:30". Trimmed reads were aligned to the Plasmodium falciparum genome (strain 3D7; version 3; release 38) using BWA-MEM (v0.7.17.2) with simple illumina mode. Then filtered for multiple mapped reads using SamTools (v1.1.2) with option "-q 1". The output file format being BAM.
Aligned BAM files were displayed using DeepTools BAMCoverage (v3.5.1.0.0) with options "--binSize 20 --smoothLength 60". The output file format being BIGWIG.
Aligned BAM files were displayed using DeepTools BAMCompare (v3.3.2.0.0) with options "--binSize 20 --scaleFactorsMethod readCount --operation log2 --pseudocount 1 --smoothLength 60". The output file format being BIGWIG.
Paired IP and Input BAM files were used to call peaks with significant enrichment in IP samples compared to the input using MACS2 (v2.1.1.20160309.6) with options "--gsize 20000000 --keep-dup 1 --qvalue 0.01 --nomodel --extsize 200 --shift 0". The narrow peaks output file format being BED.
Paired IP and Input BAM files were used to call peaks with significant enrichment in IP samples compared to the input using MACS2 (v2.1.1.20160309.6) with options "--gsize 20000000 --keep-dup 1 --qvalue 0.01 --nomodel --extsize 200 --shift 0". The peak summits output file format being BED.
Assembly: Plasmodium falciparum genome (strain 3D7; version 3; release 38)
Supplementary files format and content: BAM: BWA-MEM output files with mulltiple mapped reads filtered out
Supplementary files format and content: BIGWIG: DeepTools BAMCompare output files for Log2(IP/Input) sample display
Supplementary files format and content: BED: MACS2 outfile of narrow genomic regions ("ChIP-seq peak") significantly enriched in paired IP samples compared to Input samples
Supplementary files format and content: BED: MACS2 outfile of ChIP-seq peak summits

organism: Plasmodium falciparum

source_name: Schizont (40hpi) Parasitized Erythrocyte Cells

growth_protocol: Wild type and AP2-LT+3xHA modified parasites (3D7 strain) were cultured under standard P. falciparum culturing conditions (5% O2, 7% CO2, 37°C, RPMI 1640 media with 0.5% AlbumaxII and hypoaxanthine). No additional drug selection added to AP2-LT+3xHA modified parasites after transfection.

extract_protocol:
The ChIP-seq protocol had 5 major steps including: (1) Chemically crosslinking the all protein-protein and chromatin-protein interactions, (2) Isolation of parasite nuclei, (3) Parasite nuclei lysis with chromatin sonication, (4) Chromatin-protein complex immunoprecipitation, and (5) DNA purification. The crosslinking step included: (a) Chemical crosslinking suspended PfAP2-LTHA (or WT culture for negative control experiment) parasite culture (At least 108 40hpi (hours post invasion) schizont-stage parasites synchronized with 10% Sorbitol more than one cycle prior) with 1% formaldehyde for 10 minutes at 37°C, (b) Quench the crosslinking with 125mM Glycine on ice for 5 minutes, (c) Pellet the cells by centrifugation and lyse the red blood cells with 0.1% Saponin in 1xPBS, and (d) Wash the cells by repeated centrifugation with 1xPBS to remove the red blood cell debris. The nuclei isolation step included: (a) Resuspend parasite pellet with 109 schizonts/2mL Lysis Buffer (10mM HEPES [pH 7.9], 10mM KCl, 0.1mM EDTA [pH 8.0], 0.1mM EGTA [pH 8.0], 1mM DTT (added just before using), and 1x protease inhibitors) and incubate on ice for 30 minutes, (b) Add a final concentration of 0.25% NP-40 and incubate for 1 minute, (c) Lyse parasite membranes with pre-chilled glass dounce homogenizer for 100 strokes per 109 schizonts/2mL Lysis Buffer, and (d) Pellet the nuclei and freeze pellet at -80°C overnight. The sonication step included: (a) Resuspend parasite nuclei pellet in 500μL of Shearing Buffer (0.1% SDS, 10mM Tris [pH 8.0], 1mM EDTA, and 1x protease inhibitors) per 5x108 parasites and (b) Sonicate the chromatin until sufficiently sheared (5% duty cycle, 75W peak incident power, 200 cycles per burst, 7°C, for 5 minutes using Covaris Focus-Ultrasonicator M220). The immunoprecipitation step included: (a) Dilute the sample 1:5 with Dilution Buffer (0.01% SDS, 1.1% TritonX-100, 1.2mM EDTA, 16.7mM Tris-HCl [pH 8.1], and 150mM NaCl), (b) Reduce background signal by pre-clearing with 20μL of Protein A/G magnetic beads (Millipore 16-663) per 1mL of sample for 2 hours at 4°C with rotation, (c) Aliquot and store 1/10 of the sample for the control Input sample until after DNA elution step, (d) Remaining 9/10 of sample is immunoprecipitated with 1:1000 anti-HA antibody (0.1mg/mL Roche Rat Anti-HA High Affinity [11867423001]) overnight at 4°C with rotation, (e) Collect the immune complexes with 20μL of Protein A/G magnetic beads per 1mL of sample for 2 hours at 4°C with rotation, (f) Wash (5 minutes each) immune complexes on magnet once with Low Salt Immune Complex Wash Buffer (0.1% SDS, 1% TritonX-100, 2mM EDTA, 20mM Tris-HCl [pH 8.1], and 150mM NaCl) at 4°C with rotation, once with High Salt Immune Complex Wash Buffer (0.1% SDS, 1% TritonX-100, 2mM EDTA, 20mM Tris-HCl [pH 8.1], and 500mM NaCl) at 4°C with rotation, once with LiCl Immune Complex Wash Buffer (0.25M LiCl, 1% NP-40, 1% Deoxycholate, 1mM EDTA, and 10mM Tris-HCl [pH 8.1]) at 4°C with rotation, and twice with 1xTE at room temperature with rotation, and (g) Elution from beads with 200μL fresh Elution Buffer (0.01% SDS and 100mM NaHCO3) per 1mL of sample for 15 minutes at room temperature with rotation (also added to Input sample). The DNA purification step included: (a) Reverse-crosslink Input and IP samples with 0.2M NaCl and incubate overnight at 45°C with shaking, (b) 0.4v/v% RNaseA treat from 30 minutes at 37°C with shaking, (c) 0.3mg/mL Proteinase K treatment for 2 hours at 45°C with shaking, and (d) Purify DNA using MinElute column (Qiagen) as directed.
DNA sequencing libraries were prepared for high-throughput Illumina sequencing on the HiSeq 2500 single-end or NextSeq 2000 paired-end mode. The library prep protocol includes 6 major steps: (1) end repair of DNA fragments, (2) addition of A-tail for adaptor ligation, (3) ligation of Illumina adaptors, (4) DNA sequence size selection, (5) DNA sequence amplification by PCR, and (6) DNA sequence clean up. The 6-nt single indexed adaptors used were diluted 1:10 prior to ligation. DNA library was size selected for 250-bp sequences. Due to the A/T-richness of the P. falciparum genome, KAPA HiFi polymerase was used for amplification during PCR steps. Only 12 rounds of amplification was used for AP2-LT ChIP-seq samples (both for input and IP libraries), and 16 rounds for the no-epitope negative control. After DNA sequence clean up, completed libraries were quantified using the Qubit fluorometer for high-sensitivity DNA and library sequence length by the Agilent Bioanalyzer 1000 or Agilent TapeStation 4150.

value: 3D7 strain (AP2-LT+3xHA line)

tag: chip target

value: HA

tag: chip antibody

value: anti-HA (Roche 3F10)

tag: treatment

value: 40 hours post invasion parasites

tag: cell type

value: Parasitized Erythrocyte Cells


title: Pca_00042

source_name: Prostate cancer

tag: tissue


title: dn17

tag: strain

tag: genotype


title: Pca_00040


title: N2-RT12-78

city: Philadelphia

first: Huasheng

address: 3610 Hamilton Walk

institute: University of Pennsylvania

tag: donor id

value: thoracic 12

tag: cell identity


title: N2-RT12-77

tag: age(years)

tag: race


title: ChIP-seq on AP2-LT in a AP2-LT+3xHA 3D7 parasite line at 40hpi replicate 3 Input

treatment_protocol: At least 108 40hpi (hours post invasion) schizont-stage parasites synchronized with 10% Sorbitol more than one cycle prior

value: Input

value: No Antibody Control


title: VYS_MEHP_neg (551958A01)

source_name: MBD-cap enriched genomic DNA samples from MEHP-treated, NTD- mouse visceral yolk sacs

value: visceral yolk sac

value: mono-2-ethylhexyl phthalate (MEHP) (100ug/ml)

tag: neural tube defect status

tag: sample type

value: MBD-cap enriched fraction

value: control fraction


title: dn16

value: Liver


title: EMB_MEHP_pos (551960A03)

source_name: MBD-cap enriched genomic DNA samples from MEHP-treated, NTD+ mouse embryos

value: whole embryos

value: positive


title: VYS_CTL_neg (551959A02)

source_name: MBD-cap enriched genomic DNA samples from DMSO-treated (control), NTD- mouse visceral yolk sacs

value: dimethyl sulfoxide (DMSO) (control) (0.01% v/v)

value: negative


title: dn15


title: Pca_00039

value: Prostate cancer

value: Tumor


title: ChIP-seq on AP2-LT in a AP2-LT+3xHA 3D7 parasite line at 40hpi replicate 2 IP

value: 3D7 strain (AP2-LT+3xHA line)

value: HA

value: anti-HA (Roche 3F10)


title: N2-RT12-76

value: Dorsal root ganglia

value: Caucasian

tag: gender

value: Female

tag: region

value: thoracic 12

tag: sequencing batch

tag: dissected soma size


title: N2-RT12-75


title: EMB_CTL_neg (551962A02)

tag: exposure


title: ChIP-seq on AP2-LT in a AP2-LT+3xHA 3D7 parasite line at 40hpi replicate 2 Input

tag: chip target

value: Input

tag: chip antibody

value: No Antibody Control

value: 40 hours post invasion parasites

value: Parasitized Erythrocyte Cells


title: dn14

value: Liver


title: Pca_00038

tag: disease state

tag: cluster subtype


title: Pca_00035

tag: tissue


title: VYS_MEHP_neg (551963A03)

tag: strain

value: visceral yolk sac

value: mono-2-ethylhexyl phthalate (MEHP) (100ug/ml)

value: MBD-cap enriched fraction

value: control fraction


title: Pca_00037

value: Prostate cancer

value: Tumor


title: N2-RT12-73

tag: donor id


title: dn13

tag: genotype


title: U937_cells_UAL3

city: Medellin

first: alejandro

last: mejia

state: Antioquia

address: carrera 56A #61-24

country: Colombia

institute: University of antioquia

description:
63_1_filtered.bam
adipocytes_human_counts.txt

data_processing:
quality control with FASTQC
Trimming of adapters and bad quality nucleotides with trimmomatic
Trimmed sequences were aligned to the reference human genome (hg19) or mm38 mouse genome using STAR
Raw counts were obtained using FeatureCounts
Normalization and gene expression analysis was performed using Deseq2 R package
Assembly: GRCh38 for human and GRCm39 for mouse
Supplementary files format and content: raw counts per sample

source_name: Adipocyte

growth_protocol: 3T3-L1(CL-173TM) mouse pre-adipocytes were purchased from ATCC (Manassas, VA, USA). Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) with 10% fetal bovine serum (FBS), 2mM glutamine, 1% penicillin/streptomycin, and 25 mM glucose (Growth Medium 2 – GM2) at 37°C and 5% CO2. Differentiation was induced two days postconfluence by adding GM2 containing 0.5 mM 3-isobutyl-1-methylxanthine (IBMX), 0.25 μM dexamethasone, 2 μM Rosiglitazone, and 1 μg/ml insulin. After two days of incubation, the medium was replaced with GM2 containing 1 μg/ml insulin. Two days later, the medium was replaced by GM2 and incubated for 24 hours with the different treatments. Human primary adipocyte culture was obtained from the abdominal fat of young women. Pre-adipocytes were induced into adipocytes after 100% confluence cultured in a differentiation medium (DMEM 25 mM glucose, 10% FBS, 0.5 mM IBMX, 5 μM dexamethasone, 10 μM insulin, and 2 μM Rosiglitazone) for 7 days. The cells were incubated with DMEM, 25 mM glucose, 10% SFB, and different treatments for another 24 hours.

extract_protocol: total RNA was extracted from cells with the RNeasy kit (QIAGEN, Valencia, CA, USA). RNA quality control, library construction, and RNA sequencing using the DNBseq platform were performed by BGI Americas Corporation (Cambridge, MA, USA).

treatment_protocol: Crude extract OBE100, M1, UA, OA, and UAL were reconstituted in dimethyl sulfoxide (DMSO) at 25 mg/ml (stock solution). The final concentration of the compounds in the culture medium was OBE100 50 µg/ml, M1 39 µg/ml (UA+OA+UAL mix), UA 23.8 µg/ml, OA 7 µg/ml, and UAL 8.2 µg/ml. The concentration used for the three different triterpenes, both in the mixture called M1 and individually, were those determined in the fraction called OBE100. Three independent experiments were performed, each in triplicate.

tag: cell type

value: Adipocyte

value: WT

tag: treatment

value: UAL


title: EMB_CTL_neg (551959A01)

value: whole embryos

value: dimethyl sulfoxide (DMSO) (control) (0.01% v/v)

tag: neural tube defect status

value: negative


title: U937_cells_UA3

description:
61_1_filtered.bam
adipocytes_human_counts.txt

value: UA


title: Pca_00034


title: dn12


title: EMB_MEHP_neg (551963A01)

tag: sample type


title: N2-RT12-74

last: Yu

value: Dorsal root ganglia

tag: age(years)

tag: race

value: Caucasian

tag: gender

value: Female

value: thoracic 12

tag: cell identity


title: N2-RT12-72

tag: region

tag: sequencing batch

tag: dissected soma size

value: hPropr


title: U937_cells_M13

description:
60_1_filtered.bam
adipocytes_human_counts.txt


title: VYS_CTL_neg (551963A02)

value: visceral yolk sac

tag: exposure


title: Pca_00033

tag: disease state

tag: cluster subtype


title: VYS_CTL_neg (552455A01)

tag: strain

tag: tissue

value: MBD-cap enriched fraction


title: dn10

value: Liver

tag: genotype


title: N2-RT12-71

tag: donor id


title: VYS_MEHP_pos (551960A01)

value: mono-2-ethylhexyl phthalate (MEHP) (100ug/ml)

value: positive

value: control fraction


title: U937_cells_OBE3

description:
59_1_filtered.bam
adipocytes_human_counts.txt

tag: cell type

value: Adipocyte

value: WT

tag: treatment

value: OBE


title: EMB_MEHP_pos (551962A01)

value: whole embryos

tag: neural tube defect status

tag: sample type


title: Pca_00032

value: Prostate cancer

value: Tumor


title: N2-RT12-70

value: Dorsal root ganglia

tag: age(years)

tag: race


title: U937_cells_CA3

description:
58_1_filtered.bam
adipocytes_human_counts.txt

value: Adipocyte with fat


title: Neuro-2a_Chromseq_TAF3_rep2

city: Xi'an

first: Wei

last: Sun

state: Shaanxi

address: No. 229 Taibai North Road, Beilin District

department: College of Life Sciences and Medicine

institute: Northwest University

description:
Neuro-2a_TAF3_APEX2_rep2
Neuro-2a_Chromseq_samples_raw_counts.txt

data_processing:
The raw sequencing reads were Quality Controled by FastQC(v0.11.8).
Then, raw reads were trimmed using fastp(v0.23.1) with the options: fastp -A -f 11 -F 0 -t 0 -T 11.
Clean reads were aligned using HISAT2(v.2.1.0) to the hg19/mm10 genome with the options: hisat2 -q -t --no-unal.
The aligned reads were quantified by featureCounts(v2.0.1) using the options: featureCounts -t gene -g gene_id --extraAttributes gene_name,gene_type -s 1 -p -C
Differential expression analysis using DESeq2 (v1.34.0).
Assembly: hg19/mm10
Supplementary files format and content: tab-delimited text file include Chrom-seq three biological replicates raw counts for each sample in HCT116 cells
Supplementary files format and content: tab-delimited text file include Chrom-seq three biological replicates raw counts for each sample in NIH3T3 cells
Supplementary files format and content: tab-delimited text file include Chrom-seq three biological replicates raw counts for each sample in Neuro-2a cells
Supplementary files format and content: tab-delimited text file include Chrom-seq three biological replicates raw counts for each sample in HEK293T cells
Supplementary files format and content: tab-delimited text file include ASO_RNA-seq three biological replicates raw counts for each sample in HEK293T cells
Library strategy: Chrom-seq

growth_protocol: Plate cells co-expressing the corresponding GCN4 and APEX2 fusion constructs for 48 hours.

extract_protocol:
The total RNA was isolated by using the NEB Next Poly A+Isolation Kit (NEB, #E7490S/L).1-5 μg of total RNA was used for the construction of sequencing libraries.
Libraries were built using the Smart-seq protocol.

treatment_protocol: Cells were changed the medium to fresh medium containing 500 µM biotin-aniline and incubate at 37℃ under 5% CO2 for 30 min. Then, H2O2 was then added to each well to a final concentration of 1 mM, and the plate gently agitated for 1 min.

tag: cell line

value: Mouse neuroblastoma


title: U937_cells_CONTROL3

description:
57_1_filtered.bam
adipocytes_human_counts.txt

value: adipocyte without fat


title: Pca_00030


title: VYS_MEHP_neg (552455A03)

value: negative


title: EMB_MEHP_pos (552455A02)


title: Neuro-2a_Chromseq_TAF3_rep1

description:
Neuro-2a_TAF3_APEX2_rep1
Neuro-2a_Chromseq_samples_raw_counts.txt


title: Neuro-2a_Chromseq_TAF3_rep3

description:
Neuro-2a_TAF3_APEX2_rep3
Neuro-2a_Chromseq_samples_raw_counts.txt


title: N2-RT12-69

value: Caucasian

tag: gender

value: Female

tag: region

value: thoracic 12

tag: cell identity


title: MDA-MB-231_Ctrl_rep1

value: MDA-MB-231 cell line

tag: agent

value: PBS


title: Pca_00029

tag: disease state


title: U937_cells_UAL2

description:
56_1_filtered.bam
adipocytes_human_counts.txt

value: UAL


title: Neuro-2a_Chromseq_Control_rep3

description:
Neuro-2a_Control_APEX2_rep3
Neuro-2a_Chromseq_samples_raw_counts.txt


title: N2-RT12-68

tag: sequencing batch

tag: dissected soma size


title: Neuro-2a_Chromseq_Control_rep2

description:
Neuro-2a_Control_APEX2_rep2
Neuro-2a_Chromseq_samples_raw_counts.txt


title: Pca_00027

tag: tissue

tag: cluster subtype


title: Neuro-2a_Chromseq_Control_rep1

description:
Neuro-2a_Control_APEX2_rep1
Neuro-2a_Chromseq_samples_raw_counts.txt


title: Pca_00026


title: U937_cells_OA2

description:
55_1_filtered.bam
adipocytes_human_counts.txt

value: Adipocyte

tag: genotype

value: OA


title: Pca_00028


title: U937_cells_OBE2

description:
52_1_filtered.bam
adipocytes_human_counts.txt

tag: cell type

value: WT

value: OBE


title: N2-RT12-67

tag: donor id


title: N2-RT12-66


title: NIH3T3_Chromseq_TAF3_rep2

description:
NIH3T3_TAF3_APEX2_rep2
NIH3T3_Chromseq_samples_raw_counts.txt

value: Mouse embryonic fibroblast


title: U937_cells_UA2

description:
54_1_filtered.bam
adipocytes_human_counts.txt

tag: treatment

value: UA


title: HOXB13_TCCSUP_72h_NC3_b

city: Bandar Sunway

first: Abhi

last: Veerakumarasivam

state: Selangor

address: Jalan Universiti

country: Malaysia

institute: Sunway University

data_processing:
Base calling was performed using Illumina HiSeq Control Software.
Paired-end reads were trimmed for adaptor sequence and rRNA sequence using BBDuk software.
The clean reads were mapped to the human reference genome, GRCh37.75
Quantification of transcripts abundance from the reads was performed using Salmon’s quasi-mapping.
Genome_build: GRCh37.75
Supplementary_files_format_and_content: sf files include TPM value for each sample.

source_name: Bladder

extract_protocol:
RNA was extracted using miRNeasy Mini Kit (Qiagen, Germany) according to the manufacturer's instructions.
Libraries were prepared using TruSeq Stranded mRNA Sample Prep LS Kit (Illumina, USA) according to the manufacturer's instructions.

treatment_protocol: One group was treated with HOXA13 or HOXB13 siRNA (T), another group was treated with negative control siRNA (NC).

value: Bladder

value: Bladder cancer TCCSUP cells

value: Treated with negative control siRNA

tag: time point

value: 72 hours post transfection

tag: replicate


title: N2-RT12-65

value: Dorsal root ganglia

tag: age(years)

tag: race


title: U937_cells_CONTROL2

description:
50_1_filtered.bam
adipocytes_human_counts.txt

value: adipocyte without fat


title: U937_cells_UAL1

description:
49_1_filtered.bam
adipocytes_human_counts.txt


title: N2-RT12-62

value: Caucasian

tag: gender

value: Female


title: U937_cells_M12

description:
53_1_filtered.bam
adipocytes_human_counts.txt


title: Pca_00025

value: Prostate cancer

value: Tumor


title: NIH3T3_Chromseq_TAF3_rep3

description:
NIH3T3_TAF3_APEX2_rep3
NIH3T3_Chromseq_samples_raw_counts.txt

tag: cell line


title: NIH3T3_Chromseq_Control_rep3

description:
NIH3T3_Control_APEX2_rep3
NIH3T3_Chromseq_samples_raw_counts.txt


title: N2-RT12-61

tag: region

value: thoracic 12

tag: cell identity


title: N2-RT12-64


title: Pca_00022

tag: disease state


title: N2-RT12-63

tag: sequencing batch


title: NIH3T3_Chromseq_TAF3_rep1

description:
NIH3T3_TAF3_APEX2_rep1
NIH3T3_Chromseq_samples_raw_counts.txt


title: NIH3T3_Chromseq_Control_rep2

description:
NIH3T3_Control_APEX2_rep2
NIH3T3_Chromseq_samples_raw_counts.txt


title: U937_cells_OA1

description:
48_1_filtered.bam
adipocytes_human_counts.txt

value: Adipocyte


title: U937_cells_UA1

description:
47_1_filtered.bam
adipocytes_human_counts.txt


title: KO3 BMDM, 6 h, PAM3CSK4

city: Saint Louis

first: Hannah

last: Dorando

state: Missouri

address: 660 South Euclid Avenue, Campus Box 8118-0020-07

institute: Washington University in St. Louis

description: Sample 12

data_processing:
RNA-seq reads were aligned to the Ensembl release 101 primary assembly with STAR (v 2.7.9a1).
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount (v 2.0.32).
Isoform expression of known Ensembl transcripts were quantified with Salmon (v 1.5.23).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow-derived macrophages (BMDMs) were produced by treating bone marrow cells with the equivalent of 10 ng/mL M-CSF from CMG14-12 cells for 6 days.

extract_protocol:
RNA was isolated using an RNeasy Plus Mini kit (Qiagen, 74134).
Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

treatment_protocol: Bone marrow-derived macrophages were plated at 200,000 cells/mL and treated with PBS or 500 ng/mL PAM3CSK4 (Tocris Bioscience, 4633) for 6 hours.

value: bone marrow-derived macrophages

value: Lair1 KO

value: PAM3CSK4 6 hours


title: NIH3T3_Chromseq_Control_rep1

description:
NIH3T3_Control_APEX2_rep1
NIH3T3_Chromseq_samples_raw_counts.txt

value: Mouse embryonic fibroblast


title: HOXB13_TCCSUP_72h_NC2_b


title: HOXB13_TCCSUP_72h_NC2_a


title: HOXB13_TCCSUP_72h_NC1_b


title: N2-RT12-59

tag: dissected soma size


title: U937_cells_OBE1

description:
45_1_filtered.bam
adipocytes_human_counts.txt

value: WT

value: OBE


title: N2-RT12-58

tag: tissue


title: KO3 BMDM, 6 h, PBS

description: Sample 11

value: PBS 6 hours


title: U937_cells_M11

description:
46_1_filtered.bam
adipocytes_human_counts.txt


title: HOXB13_TCCSUP_72h_NC3_a

value: Bladder

value: Bladder cancer TCCSUP cells

value: Treated with negative control siRNA


title: HOXB13_TCCSUP_72h_NC1_a

value: 72 hours post transfection


title: N2-RT12-60

value: Dorsal root ganglia

value: Caucasian


title: KO2 BMDM, 6 h, PAM3CSK4

description: Sample 10


title: U937_cells_CA1

description:
44_1_filtered.bam
adipocytes_human_counts.txt

value: Adipocyte with fat


title: U937_cells_CONTROL1

description:
43_1_filtered.bam
adipocytes_human_counts.txt

value: adipocyte without fat


title: N2-RT12-57

value: Female

value: thoracic 12

value: hPropr


title: N2-RT12-56


title: N2-RT12-55


title: HOXB13_TCCSUP_72h_T2_a

value: Treated with HOXB13 siRNAs


title: KO2 BMDM, 6 h, PBS

description: Sample 9

value: bone marrow-derived macrophages

value: Lair1 KO


title: HOXB13_TCCSUP_72h_T2_b


title: Mononuclear cells, relapse, TMR, S18

city: Old Al rayyan

first: Nisar

last: Ahmed

state: Doha

address: LAS Building, Education city

department: College of Health and Life Sciences

country: Qatar

institute: Hamad Bin Khalifa University

description: ATAC-seq

data_processing:
ATAC-seq libraries underwent FastQC testing for quality assessment. Trimmomatic was employed with default parameters to filter low-quality reads and remove TruSeq adaptors. The processed reads were aligned to the hg38 human genome using Bowtie2, and SAM files were converted to BAM format using samtools. Mitochondrial, duplicate, and blacklisted reads were subsequently removed. Reads were adjusted for tn5 binding using the alignmentSieve tool. Finally, peaks were called on the processed BAM files using the callpeak and BAMPE commands of the MACS2 peak calling algorithm.
Assembly: Hg38
Supplementary files format and content: NarrowPeak

source_name: Relapse

growth_protocol: Flash-frozen mononuclear cells from bone marrow and/or peripheral blood of adult AML diagnosis and relapse pair samples were maintained in IMDM supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
The Active Motif ATAC-seq kit was used to perform ATAC-seq on MNCs. 1 × 10^5 cells were first pelleted and washed with ice-cold PBS. Subsequently, the cells were re-suspended in an ice-cold ATAC-Lysis buffer. Next, for tagmentation the isolated nuclei were incubated at 37°C for precisely 30 minutes.
In ATAC-seq, treated DNA was purified using the Zymo DNA Clean and Concentrator-5 Kit. Subsequently, tagmented libraries underwent PCR amplification with 10 cycles and were size-selected using 60µl SPRI beads.

treatment_protocol: Cryopreserved bone marrow samples were slowly thawed using IMDM supplemented  with 10% FBS and DNAse. Viability was calculated under a hemocytometer with trypan blue – samples with a viability <80% were subjected to a dead cell sort using MACS dead cell removal kit (cat: 130-090-101)

value: Relapse

tag: disease

value: AML

value: Mononuclear cells


title: KO1 BMDM, 6 h, PAM3CSK4

description: Sample 8

tag: genotype

value: PAM3CSK4 6 hours


title: HOXB13_TCCSUP_72h_T1_b

value: Bladder

value: Bladder cancer TCCSUP cells


title: N2-RT12-54

source_name: Dorsal root ganglia


title: Mononuclear cells, diagnosis, TMD, S17

description: ATAC-seq

source_name: Diagnosis

value: Diagnosis

tag: cell type


title: KO1 BMDM, 6 h, PBS

description: Sample 7

value: PBS 6 hours


title: N2-RT12-53

value: Dorsal root ganglia

tag: donor id

value: Caucasian


title: HOXB13_TCCSUP_72h_T1_a

tag: treatment

value: 72 hours post transfection


title: Mononuclear cells, relapse, MBR, S16

description: ATAC-seq


title: N2-RT12-52

value: Female