title: CMPD1_MDAMB231_1

description:
Library name: CMPD1_MDAMB231_1
DK24082_04


title: IMR5 - dmso_rep1

status: Public on May 19 2025

type: SRA

city: bethesda

first: Jack

last: Shern

state: MD

address: 10 Center drive

country: USA

institute: NCI

library_source: transcriptomic

data_processing:
Illumina RTA v3.4.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg19 whole genome using STAR 2.7.3a built in Partek Flow
DESeq2 package was used to normalize counts using the Partek E/M model
Genome_build: hg19

molecule: total RNA

organism: Homo sapiens

source_name: IMR5, MYCN-amplified

growth_protocol: IMR5 cells are grown in RPMI media supplemented with 10% fetal bovine serum, penicillin/streptomycin, and glutamine. They are split every 3-4 days.

extract_protocol:
Total mRNA was extracted using the RNeasy Plus Mini Kit (Qiagen) as per the manufacturer’s protocol.
Strand-specific whole transcriptome sequencing libraries were prepared using the TruSeq® Stranded Total RNA LT Library Prep Kit (Illumina) by following the manufacturer’s procedure.

treatment_protocol: Selinexor treated cells were grown in media with 100nM of selinexor for 24 hours prior to RNA extraction. Control cells were growin media supplemented with DMSO. In the XPO1 knockdown cells, IMR5 cells were nucleofected with #10 ON-TARGETplus siRNAs targeting XPO1. Negative control siRNAs were obtained from Horizon (Cat. # LQ-003030-00-000) and transiently transfected into IMR-5 cells using the Nucleofector with solution L and program C-005 (Amaxa Biosystems). RNA was extracted from the transfected cells after 72 hours

tag: tissue

value: Neuroblastoma cell line

tag: cell line

tag: treatment

value: dmso


title: AorticValve, Exp, 4 weeks, Rep 1

city: Athens

first: Nikolaos

last: Anousakis-Vlachochristou

address: Vas Sofias 114 Ave

department: First Department of Cardiology, Athens Medical School

country: Greece

institute: National and Kapodistrian University of Athens

data_processing:
SmallRNA-Seq lane FASTQ files were merged through concatenation. Data processing was performed using DIANA-mAP (v1.0), a fully automated computational pipeline with an emphasis on preprocessing, allowing for miRNA NGS data analysis from the raw data for quantification and differential expression. Preprocessing was performed with the external tools FastQC (v0.11.7), DNApi (v1.1), and Cutadapt (v1.16). The raw datasets were quality checked, allowing a minimum Phred score of 10, while adapters were provided by the NEBNext manuals and trimmed using a 10 bp minimum allowed read length after trimming. Reads were subsequently aligned to the Oryctolagus Cuniculus GCF_009806435.1 genome assembly from RefSeq using Bowtie (v1.1.1), allowing up to five multiple maps per read. Aligned reads were quantified through miRDeep2 (v0.0.8) using the miRBase v22 hairpin and mature Oryctolagus Cuniculus miRNA forms, allowing one mismatch on the precursor during alignment. Finally, differential expression analysis between the various time points was performed based on the negative binomial distribution using DESeq2 (v1.30.1). The parameters of the remaining DIANA-mAP and external tools were set to their default values.
Assembly: Oryctolagus Cuniculus GCF_009806435.1
Supplementary files format and content: tab-delimited text file with raw counts per Sample

organism: Oryctolagus cuniculus

source_name: Aortic Valve

extract_protocol:
small RNA was extracted using Trizol
small RNA-Seq libraries were prepared using the NEBNext Multiplex Small RNA Library Prep kit for Illumina. NGS Sequencing was performed on a Nova-Seq 6000 System (Illumina), which produced an average sequencing depth of 2.2 million 68 bp single-end reads for the sRNA-Seq data.

treatment_protocol: At sacrifice, one aortic valve cusp was dissected, separated from most of the surrounding fat using magnifying lenses, cleaned from blood in normal saline buffered heparin solution and immersed in RNAlater. All procedures was done in a glass bench using sterilized forceps and scissors, all material was thoroughly cleaned from RNAses using RNAse OFF (Takara Bio) and excessive detergent removed with water for injection. The RNAlater-preserved samples were stored at 4 C for 24 hours and then transferred at - 75 C for long-term storage.

value: Aortic Valve

tag: genotype

value: WT

value: 1% cholesterol + 3500 IUs ergocalciferol


title: Myocardium, Experimental, Replicate 2

description:
RNAseq_myocardium_raw_counts.txt
1059-MYO_S27

data_processing:
RNA-Seq lane FASTQ files were merged through concatenation. Data were preprocessed by utilizing FastQC (v0.11.9) for quality control with a minimum quality score of 10 and by removing the NEBNext adapters using TrimGalore (v0.6.6), introducing a minimum read length allowance of 20 bp. Using the Oryctolagus Cuniculus GCF_009806435.1 genome assembly and annotations from RefSeq, reads were subsequently aligned using STAR (v2.7.8a). Aligned reads were quantified through RSEM (v1.3.3) using RefSeq annotations. Finally, the R package edgeR (v3.42.4) was used for the assessment of DEGs between time points by fitting a quasilikelihood negative binomial generalized log-linear model to the count data (glmQLFit function), which was robust to potential outliers. Prior to the statistical analyses, expression measurements were normalized to account for library depth (counts per million, CPM), while between-library normalization scaling factors were calculated by implementing the trimmed mean of M-values method. Finally, genes with consistently low expression values among the majority of observed samples were filtered out (with the filterByExpr function).
Assembly: Oryctolagus Cuniculus GCF_009806435.1
Supplementary files format and content: tab-delimited text file with raw counts per Sample

source_name: Myocardium

extract_protocol:
RNA was extracted using Trizol
RNA sequencing libraries were prepared using the NEBNext Ultra II directional RNASeq kit. NGS Sequencing was performed on a Nova-Seq 6000 System (Illumina), which produced an average sequencing depth of 21.2 million 100 bp single-end reads for the RNA-Seq data.

value: Myocardium


title: WT-GL261-0Gy-rep1

type: RNA

city: Irvine

first: Robert

middle: Paul

last: Krattli Jr

state: CA

address: 811 Health Sciences Road, MedSci B-120

department: Anatomy and Neurobiology

institute: University of California, Irvine

description: Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material

hyb_protocol: For each 12-lane cartridge, 70 µl of Master Mix were combined with 42 µl of the fluorescent labeled Reporter CodeSet, flicked to mix, and briefly spun down before 8 µl of combined solution were added to each lane. 5 µl of total RNA (20 ng/µl) per sample was then added to individual lanes. Next, 2 µl of the biotin Capture ProbeSet was added to each lane. Then, loaded cartridges were placed in a thermocycler at 65 degrees Celsius for approximately 20 hours. Following hybridization, cartridges are loaded onto nCounter Prep Station (NanoString™) to perform liquid transfers, magnetic bead separations, and immobilization of molecular labels on the sample cartridge surface. Protocol as described per the manufacture’s instructions: NanoString™ (Seattle, WA).

scan_protocol: Scanning of hybridized cartridges was performed on an nCounter Digital Analyzer (NanoString™) per the manufacturer’s instructions: NanoString™ (Seattle, WA).

data_processing: The raw value data were normalized utilizing a two-step normalization process: an initial Positive Control Normalization, followed by a CodeSet Content Normalization using 13 internalized housekeeping genes that accompanied the Neuroinflammation Panel. Both processes were performed by the nSolver Analysis Software 4.0 (NanoString™).

label: Color-Coded Reporter Probe

organism: Mus musculus

source_name: fresh-frozen brain tissue

label_protocol: 5 µl of total RNA (20 ng/µl) per sample were labeled with a fluorescent Reporter ProbeSet per the manufacturer’s instructions: NanoString™ (Seattle, WA).

extract_protocol: Total RNA was isolated from 100 mg of fresh-frozen brain tissue per sample. Brain samples were first homogenized in QIAzol Lysis Reagent (Qiagen) and then underwent RNA isolation with RNeasy Plus Universal Mini Kit (Qiagen) to obtain a minimum of 100 ng of unreplicated RNA, whose purity was verified with both NanoDrop (ThermoFisher) and Bioanalyzer 2100 (Agilent Technologies).

value: fresh-frozen brain tissue

tag: Sex

value: male

tag: strain

tag: tumor induction

value: Yes

tag: tumor cell line

tag: radiation dose

value: 0 Gy

tag: pmx205 drug tx

value: No


title: Control_MDAMB231_3

city: Grand Forks

first: Motoki

last: Takaku

state: ND

address: W221 Biomedical Sciences 1301 N. Columbia Road

institute: University of North Dakota

description:
Library name: Control_MDAMB231_3
DK24082_03

data_processing:
Adapter sequences were removed using Cutadapt, and the reads were subsequently mapped to the GRCH 38 genome using HISAT2 aligner. Read counts for each gene were collected by featureCounts. Differentially expressed genes were identified with DESeq2 using filtering thresholds of FDR < 0.05. Pathway enrichment analysis was perfored by DAVID.
Assembly: GRCH38
Supplementary files format and content: txt, csv

molecule: polyA RNA

source_name: breast cancer

extract_protocol:
RNAs were purified by the RNeasy Mini Kit (Qiagen).
RNA-seq library preparation was conducted with the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (LEXOGEN), and the libraries were sequenced on a NextSeq500.

value: breast cancer

tag: cell type

value: luminal


title: WT-0Gy-rep3


title: Myocardium, Experimental, Replicate 1

description:
RNAseq_myocardium_raw_counts.txt
E33-MYO_S25


title: BatchB Vehicle (DMSO) rep2

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

description: Library name: sample B1-2-1

data_processing:
Quality of RNA-seq raw data was assessed using FastQC (v0.11.9), and the common regions of MGISEQ adapter sequences were removed using TrimGalore (v0.6.6). The trimmed reads were then aligned to the human reference genome hg38 using the STAR (v2.7.9a) with default settings. Transcript abundance per gene including expected read counts and transcripts per million (TPM) were quantified using RSEM (v1.3.3) with gene annotation GRCh38.84.
Assembly: GRCh38.84
Supplementary files format and content: tab-delimited text files include Expected counts for each Sample

growth_protocol: Human astrocytoma cell line, SW1783 (HTB-13) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). SW1783 cells were maintained in Leibovitz's L-15 medium supplemented with 10% (v/v) heat-inactivated FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37 °C, 0% CO2 incubator. The cell was subcultured every 3 or 4 days, depending on the cell density.

extract_protocol:
Total RNA was isolated according to the manufacturer’s protocol. The concentration of the isolated RNA was determined using an Agilent RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany), and RNA quality was evaluated by assessing the RNA integrity number (RIN > 7).
A total RNA (1 microgr) was processed to prepare a mRNA sequencing library using the MGIEasy RNA Directional Library Prep kit (#1000006386, MGI Tech Co., Ltd., China) according to the manufacturer’s instruction. The library was quantified using the QauntiFluor® ssDNA System (E3190, Promega Corporation, WI, USA). The prepared DNA nanoball was sequenced on the MGIseq system (MGI Tech Co., Ltd., China) with 100 bp paired-end reads.

treatment_protocol: Leibovitz's L-15, phosphate-buffered saline (PBS), TrypLE Express, penicillin-streptomycin, and fetal bovine serum (FBS) were purchased from Gibco (Grand Island, NY, USA). Cell culture flasks and multiwell culture plates were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Dimethyl sulfoxide (DMSO) and QIAzol lysis reagents were purchased from Sigma-Aldrich (St. Louis, MO, USA) and Qiagen (Germantown, MD, USA), respectively. The dried medicinal plants, prepared in compliance with the Korean Pharmacopoeia, were supplied from Kwangmyung-dang Medicinal Herbs Co. (Ulsan, Republic of Korea). The samples used in the experiment underwent organoleptic examination by Dr. Choi Goya, an herbal medicine organoleptic examination expert appointed by the Korea Food and Drug Administration, and were additionally identified at the species level by analyzing the DNA barcode region sequences. Voucher specimen were deposited in the Korean Herbarium of Standard Herbal Resources, Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Republic of Korea . All herbs and extracts can be obtained from the Oriental Medicine Resources Research Center (KIOM, https://oasis.kiom.re.kr/herblib). A hot water and 70% ethanol extract of each plant was prepared and supplied by KOC Biotech Co. (Daejeon, Republic of Korea). Briefly, dried plants (1,000 g) were pulverized and extracted in hot distilled water (10 L) for 3 h under a reflux extraction system (MS-DM609; MTOPS, Seoul, Republic of Korea) or in 70% ethanol (15L) for 1 h under ultrasonication system (VCP-20, Lab companion, Dajeon, Republic of Korea) twice. The extract solution was filtered through a 5 µm cartridge filter, concentrated in a rotary evaporator (Ev-1020, SciLab, Seoul, Republic of Korea), and then lyophilized in a freeze dryer (LP-20, Ilshin-Bio-Base, Dongduchen, Republic of Korea) to obtain the final extract. The extract was finely homogenized and packed in a glass bottle containing a desiccant silica gel. The decoction was prepared by mixing each extract, considering the composition ratio and extract yield of a single medicinal herb, and homogenized, according to the Korean Pharmacopoeia. For the in vitro treatment, extracts (100 mg) were vigorously vortexed for 30 min in 10 mL phosphate-buffered saline (PBS; Thermo Fisher Scientific, Rockford, IL, USA) containing 2% DMSO and then sterilized by filtering through a 0.22 µm membrane to obtain a stock solution (10 mg/mL); the stock solution was aliquoted in small volumes and stored at -80°C until use.

value: 0.1% DMSO

tag: batch

value: B


title: BatchB Vehicle (DMSO) rep1

description: Library name: sample B1-1-1


title: WT-0Gy-rep2


title: Myocardium, Control, Replicate 3

description:
RNAseq_myocardium_raw_counts.txt
C49-MYO_S29

value: normal chaw


title: Control_MDAMB231_1

description:
Library name: Control_MDAMB231_1
DK24082_01


title: Myocardium, Control, Replicate 1

description:
RNAseq_myocardium_raw_counts.txt
C42-MYO_S20


title: Myocardium, Control, Replicate 2

description:
RNAseq_myocardium_raw_counts.txt
C43-MYO_S28


title: BatchA water extract of Schisandrae Fructus  (Low dose) rep3

description: Library name: sample 2-3-6

value: Schisandrae Fructus water extract 20 μg/mL

value: A


title: TOF-023-W8

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38 p10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Sigma

extract_protocol:
Colon biopsies from patients with active UC starting tofacitinib were collected at baseline (n=11) and during follow-up (n=12), placed immediately in cold Hank’s Balanced Salt Solution (HBSS) (Gibco, MA, USA) and kept at 4º until processing (<1 h). Freshly collected biopsies were washed with HBSS/DTT (Roche, Spain) 5mM for 15 min and then washed in complete medium (CM) (RPMI 1640 medium (Lonza, MD, USA) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Biosera, France), 100U/ml penicillin, 100 U/ml streptomycin and 250 ng/ml amphotericin B (Lonza), 10µg/ml gentamicin sulfate (Lonza) and 1,5mM Hepes (Lonza) for 10 minutes. Both incubations were performed at room temperature in a platform rocker. Biopsies were chopped with a scalpel and placed into tubes containing 500 μl of Digestion Solution (CM + Liberase TM (0.5 Wünsch units/ml) (Roche, Spain) + DNase I (10 μg/mL) (Roche, Spain) and incubated on a shaking platform for 1h at 250rpm at 37ºC. After incubation biopsies were filtered 2 times through a 50-μm cell strainer and 3 times through a 30-μm cell strainer (CellTrics, Sysmex, USA), washed with Dulbecco’s Phosphate Buffered Saline (PBS; Gibco, USA) and resuspended in RPMI (Roswell Park Memorial Institute) medium supplemented with 0.05% of Bovine fetal serum (BSA) at a final concentration of ~500.000-1·106 cells/mL (Veny et al, JCC 2020).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode.

tag: patient

value: female

tag: timepoint

tag: group

value: Responder

value: Sigma

value: post-tx


title: WT-GL261-0Gy-rep2


title: BatchA water extract of Schisandrae Fructus  (Medium dose) rep3

description: Library name: sample 2-3-5

value: Schisandrae Fructus water extract 100 μg/mL


title: Ascending Aorta, Experimental, Replicate 2

description:
RNAseq_ascending_aorta_raw_counts.txt
E43-AORTA_S23

source_name: Ascending Aorta

value: Ascending Aorta

value: WT

value: 1% cholesterol + 3500 IUs ergocalciferol


title: BatchA water extract of Schisandrae Fructus  (High dose) rep3

description: Library name: sample 2-3-4

value: Schisandrae Fructus water extract 500 μg/mL


title: BatchB Vehicle (DMSO) rep3

description: Library name: sample B1-3-1


title: BatchA water extract of Schisandrae Fructus  (Low dose) rep2

description: Library name: sample 2-2-6


title: TOF-022-W0

description: 10x Genomics

source_name: Descending colon

value: male

value: No responder

value: Descending colon

value: pre-tx


title: TOF-019-W16

description: 10x Genomics


title: BatchA water extract of Schisandrae Fructus  (Medium dose) rep2

description: Library name: sample 2-2-5


title: BatchB ethanol extract of Schisandrae Fructus (High dose) rep1

description: Library name: sample 9-1-4

value: Schisandrae Fructus ethanol extract 310 μg/mL

value: B


title: Ascending Aorta, Experimental, Replicate 1

description:
RNAseq_ascending_aorta_raw_counts.txt
E25-AORTA_S21


title: Ascending Aorta, Control, Replicate 3

description:
RNAseq_ascending_aorta_raw_counts.txt
C32-AORTA_S24

value: normal chaw


title: BatchA water extract of Schisandrae Fructus  (High dose) rep2

description: Library name: sample 2-2-4

value: A


title: TOF-019-W8

description: 10x Genomics


title: Ascending Aorta, Control, Replicate 2

description:
RNAseq_ascending_aorta_raw_counts.txt
C36-AORTA_S22


title: Control_MDAMB231_2

description:
Library name: Control_MDAMB231_2
DK24082_02

value: breast cancer

value: luminal


title: TOF-019-W0

description: 10x Genomics

value: Sigma


title: WT-0Gy-rep1

value: fresh-frozen brain tissue

value: No

value: 0 Gy


title: TOF-023-W0

description: 10x Genomics

value: female

value: Responder


title: BatchA water extract of Schisandrae Fructus  (Low dose) rep1

description: Library name: sample 2-1-6

value: Schisandrae Fructus water extract 20 μg/mL


title: BatchA water extract of Schisandrae Fructus  (Medium dose) rep1

description: Library name: sample 2-1-5

value: Schisandrae Fructus water extract 100 μg/mL


title: Ascending Aorta, Control, Replicate 1

description:
RNAseq_ascending_aorta_raw_counts.txt
C35-AORTA_S18

value: Ascending Aorta

value: WT


title: AorticValve, Control, 2 weeks, Replicate 1

description:
RNAseq_aortic_valve_raw_counts.txt
RNAseq_aortic_valve_raw_counts_myocardium_genes_filtered.txt
C45_S34

value: Aortic Valve


title: TOF-016-W8

description: 10x Genomics

source_name: Rectum

value: No responder

value: Rectum

value: post-tx


title: TOF-016-W0

description: 10x Genomics

value: pre-tx


title: BatchA water extract of Schisandrae Fructus  (High dose) rep1

description: Library name: sample 2-1-4

value: Schisandrae Fructus water extract 500 μg/mL

value: A


title: COR.KO.F77-2

city: Lleida

first: Daniel

last: Sanchis

address: Av. Rovira Roure, 80

department: Ciències Mèdiques Bàsiques

institute: Universitat de LLeida - IRBLleida

description: gene expression data from adult Tatd knockout mouse

hyb_protocol: Labeled cDNA was hybridizated in Mouse Clariom S Thermofisher microarrays for 16 hours with rotation

scan_protocol: Microarrays were scanned in Affymetrix Genechip Scanner 3000

data_processing: The images were processed with the Affymetrix GeneChip Command Console software (Affymetrix) for CEL file generation. To check the array quality, TAC software was used. Samples that demonstrated good quality results (pm mean, bgrd mean, pos vs neg auc, ...) were subjected to subsequent analysis. Raw expression values were obtained directly from .CEL files were preprocessed using the RMA normalization method.  Statistical language R and Bioconductor associated packages were used to process data.

label: biotin

source_name: cardiac ventricle tatd-/- female

label_protocol: Samples were amplified with WT Amplification kit (Thermofisher) and fragmented and labelled with WT Terminal labeling kit (Thermofisher)

growth_protocol: Adult mice

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and retro-transcribed

treatment_protocol: cervical dislocation, tissues were extracted, rinsed in cold PBS and frozen in liquid nitrogen, stored at -80ºC until used for total RNA extraction

tag: gender

value: tatd-/-

value: Heart

tag: age

value: Adult (2 months)


title: COR.KO.F77-3

tag: tissue


title: COR.KO.M78-1

source_name: cardiac ventricle tatd-/- male

value: male


title: COR.KO.M77-1


title: TOF-015-W8

description: 10x Genomics

value: female

value: Sigma


title: AorticValve, Control, 7 weeks, Replicate 3

description:
RNAseq_aortic_valve_raw_counts.txt
RNAseq_aortic_valve_raw_counts_myocardium_genes_filtered.txt
C43_S33

value: normal chaw


title: COR.WT.F76-3

description: gene expression data from adult wild type mouse

source_name: cardiac ventricle tatd+/+ female

value: wild type


title: COR.WT.F76-2


title: BatchA Vehicle (DMSO) rep3

description: Library name: sample A1-3-1

tag: cell line

value: 0.1% DMSO


title: TOF-015-W0

description: 10x Genomics

value: Responder

tag: treatment


title: AorticValve, Control, 7 weeks, Replicate 2

description:
RNAseq_aortic_valve_raw_counts.txt
RNAseq_aortic_valve_raw_counts_myocardium_genes_filtered.txt
C42_S32

value: Aortic Valve

tag: genotype

value: WT


title: COR.KO.F77-1


title: AorticValve, Control, 7 weeks, Replicate 1

description:
RNAseq_aortic_valve_raw_counts.txt
RNAseq_aortic_valve_raw_counts_myocardium_genes_filtered.txt
C38_S31


title: BatchA Vehicle (DMSO) rep2

description: Library name: sample A1-2-1


title: AorticValve, Exp, 2 weeks, Replicate 4

description:
RNAseq_aortic_valve_raw_counts.txt
RNAseq_aortic_valve_raw_counts_myocardium_genes_filtered.txt
E41_S29

value: 1% cholesterol + 3500 IUs ergocalciferol


title: BatchA Vehicle (DMSO) rep1

description: Library name: sample A1-1-1


title: TOF-013-W0

description: 10x Genomics

tag: Sex

value: No responder


title: TOF-013-W8

description: 10x Genomics

value: post-tx


title: AorticValve, Exp, 2 weeks, Replicate 3

description:
RNAseq_aortic_valve_raw_counts.txt
RNAseq_aortic_valve_raw_counts_myocardium_genes_filtered.txt
E40_S28


title: COR.KO.M78-0


title: activated KIKO T cells-3

city: Tokushima

first: Junko

last: Morimoto

address: 3-18-15 Kuramoto-cho

country: Japan

institute: Tokushima University

description: Library name: Sample 12

data_processing:
The quarity of raw sequence fastq-formatted files were assessed by FastQC (v0.11.9).
Sequences were trimmed using Cutadapt (v2.9) to  get high quality clean data.
Trimmed sequence reads were mapped to  GRCm39/mm10 using Hisat2 (v 2.2.0).
Assembly: GRCm39
Supplementary files format and content: txt files containing FPKM values for each sample.

source_name: splenic  CD4 T cell

extract_protocol:
Total RNA was prepared using Rneasy Mini Kit (GIAGEN). 15ng total RNA was used for the isolation of poly(A)+ RNA by NEBNext Poly(A) mRNA magnetic isolation kit (New England Biolbs) following manufactures's protocols.
Libraries were prepared by TaKaRa SmartSeq Standed Kit following manufacture's protocols.

treatment_protocol: For T cell activation, splenic naïve CD4 T cells were activated with Dynabeads mouse T-Activator CD3/CD28 for 16 hours.

value: splenic  CD4 T cell

value: anti-CD3/CD28 stimulation


title: AorticValve, Exp, 2 weeks, Replicate 2

description:
RNAseq_aortic_valve_raw_counts.txt
RNAseq_aortic_valve_raw_counts_myocardium_genes_filtered.txt
E39_S27


title: TOF-012-W16

description: 10x Genomics


title: COR.WT.M75-1

source_name: cardiac ventricle tatd+/+ male


title: COR.WT.F76-1


title: AorticValve, Exp, 2 weeks, Replicate 1

description:
RNAseq_aortic_valve_raw_counts.txt
RNAseq_aortic_valve_raw_counts_myocardium_genes_filtered.txt
E25_S30


title: activated KIKO T cells-1

description: Library name: Sample 10


title: COR.WT.M75-0


title: TOF-012-W0

description: 10x Genomics

value: pre-tx


title: NE.KO.F77-3

source_name: brain cortex tatd-/- female

value: tatd-/-

value: brain cortex


title: naïve KIKO CD4 T cells-3

description: Library name: Sample 9

value: naïve


title: TOF-011-W8

description: 10x Genomics

value: male


title: NE.KO.F77-2

value: female

value: Adult (2 months)


title: naïve KIKO CD4 T cells-2

description: Library name: Sample 8


title: TOF-011-W0

description: 10x Genomics

value: Sigma


title: AorticValve, Exp, 4 weeks, Replicate 3

description:
RNAseq_aortic_valve_raw_counts.txt
RNAseq_aortic_valve_raw_counts_myocardium_genes_filtered.txt
E37_S37


title: naïve KIKO CD4 T cells-1

description: Library name: Sample 7


title: AorticValve, Exp, 4 weeks, Replicate 2

description:
RNAseq_aortic_valve_raw_counts.txt
RNAseq_aortic_valve_raw_counts_myocardium_genes_filtered.txt
E35_S36


title: TOF-010-W0

description: 10x Genomics

value: Rectum


title: COR.WT.M75-2

value: wild type

value: Heart


title: TOF-012-W8

description: 10x Genomics

value: Responder


title: activated KI CD4 T cells-3

description: Library name: Sample 6


title: TOF-009-W48

description: 10x Genomics


title: AorticValve, Exp, 4 weeks, Replicate 1

description:
RNAseq_aortic_valve_raw_counts.txt
RNAseq_aortic_valve_raw_counts_myocardium_genes_filtered.txt
E26_S21

value: Aortic Valve

value: WT

value: 1% cholesterol + 3500 IUs ergocalciferol


title: AorticValve, Exp, 4 weeks, Replicate 4

description:
RNAseq_aortic_valve_raw_counts.txt
RNAseq_aortic_valve_raw_counts_myocardium_genes_filtered.txt
E38_S38


title: AorticValve, Exp, 7 weeks, Replicate 4

description:
RNAseq_aortic_valve_raw_counts.txt
RNAseq_aortic_valve_raw_counts_myocardium_genes_filtered.txt
E33_S1


title: NE.KO.M78-1

source_name: brain cortex tatd-/- male


title: TOF-009-W0

description: 10x Genomics


title: NE.WT.F76.3

source_name: brain cortex tatd+/+ female


title: NE.KO.M78-0


title: NE.KO.M77-1


title: activated KI CD4 T cells-1

description: Library name: Sample 4

value: splenic  CD4 T cell


title: activated KIKO T cells-2

description: Library name: Sample 11

value: anti-CD3/CD28 stimulation


title: AorticValve, Exp, 7 weeks, Replicate 2

description:
RNAseq_aortic_valve_raw_counts.txt
RNAseq_aortic_valve_raw_counts_myocardium_genes_filtered.txt
1062_S2


title: naïve KI CD4 T cells-3

description: Library name: Sample 3


title: AorticValve, Exp, 7 weeks, Replicate 3

description:
RNAseq_aortic_valve_raw_counts.txt
RNAseq_aortic_valve_raw_counts_myocardium_genes_filtered.txt
1063_S3


title: NE.WT.F76-2


title: TOF-005-W24

description: 10x Genomics

value: No responder

value: post-tx


title: naïve KI T CD4 cells-2

description: Library name: Sample 2


title: NE.WT.F76-1

value: brain cortex


title: AorticValve, Exp, 7 weeks, Replicate 1

description:
RNAseq_aortic_valve_raw_counts.txt
RNAseq_aortic_valve_raw_counts_myocardium_genes_filtered.txt
1059_S4


title: naïve KI CD4 T cells-1

description: Library name: Sample 1

value: naïve


title: TOF-005-W0

description: 10x Genomics

value: male

value: pre-tx


title: activated KI CD4 T cells-2

description: Library name: Sample 5


title: W-9M-3

status: Public on May 18 2025

city: WuHan

first: Yi-Xuan

last: Tu

state: HuBei

address: 1 Shizishan Rd

department: College of Life Science and Technology

country: China

institute: Huazhong agricultural university

description: Library name: W3_1_m9

data_processing:
FastQC was used to check the quality of the raw sequence fastq files. High-quality pruning was performed using fastp. Paired end reads were mapped to the reference genome of Ensembl (GRCm39) using HISAT2. And SAMtools is used to sort and index aligned BAM files. Reads were counted using the featureCounts program in the Subread.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: ovary

extract_protocol: Following manufacturer's protocol, the total RNA of sample was extracted using Trizol reagent. After Sample QC, the mRNA was hybridized with Oligo（dT）probe and Captured by Magnetic Beads. The mRNA was then reverse-transcripted to first strand DNA.First strand DNA was used as template to synthesis second strand DNA, obtaining dsDNA. The dTTP tailed adaptor was ligated to both ends of the dsDNA fragments. The ligation product was amplified by PCR, and circularized to get single-stranded circular(ssCir) library. The ssCir library was then amplified through rolling circle amplification (RCA) to obtain DNA nanoball(DNB). The DNB was then loaded to flowcell, and sequenced by DNBSEQ Platform.

value: ovary

value: female

value: white brown rice


title: W-9M-1

description: Library name: W1_1_m9


title: W-9M-2

description: Library name: W2_1_m9


title: NE.WT.M75-1

source_name: brain cortex tatd+/+ male

value: wild type

value: Adult (2 months)


title: P-9M-3

description: Library name: P3_1_m9

value: polished rice


title: NE.WT.M75-2


title: P-9M-2

description: Library name: P2_1_m9


title: P-9M-1

description: Library name: P1_1_m9


title: NE.WT.M75-0


title: B-9M-3

description: Library name: B3_1_m9

value: black rice


title: B-9M-2

description: Library name: B2_1_m9


title: B-9M-1

description: Library name: B1_1_m9


title: W-6M-2

description: Library name: W_m6_2


title: P-6M-3

description: Library name: P_m6_3


title: W-6M-3

description: Library name: W_m6_3


title: W-6M-1

description: Library name: W_m6_1


title: TOF-005-W8

description: 10x Genomics

value: Rectum


title: P-6M-1

description: Library name: P_m6_1


title: B-6M-3

description: Library name: B_m6_3


title: P-6M-2

description: Library name: P_m6_2


title: B-6M-2

description: Library name: B_m6_2


title: B-6M-1

description: Library name: B_m6_1


title: TPE_antiTFAP2C_rep3

city: Chengdu, China

first: Ailing

last: Zhong

state: Sichuan

address: No.17 Renmin road section3

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

institute: Sichuan University

description: Gastric organoids, Trp53-/-;sgPten;sgEzh2, rep3

library_source: genomic

data_processing:
The Illumina NovaSeq 6000 platform was employed to perform genomic sequencing. Following quality control by the fastp standard workflow, the Bowtie2 software was utilized to construct an index for the mouse genome (mm10) and align paired-end clean data of 150 bp length using the options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700". The SAMtools program was utilized to convert sam files to sorted bam files. Picard's MarkDuplicates tool was used to remove duplicates with the option "REMOVE_DUPLICATES=true". Normalized bw files were generated using deepTools with the option "bamCoverage -bs=1 --normalizeUsing BPM" for further visualization in the Integrated Genome Viewer (IGV). Peak calling was performed using the MACS2 software with the option "macs2 callpeak --broad -q 1e-2 -f BAMPE -g mm --keep-dup all". ChIPseeker was employed to identify the genomic distribution of the peaks, with the TSS region "tssRegion" set as (-3000, 3000) for annotation. The "narrowPeak" files were transformed into GrangesList forms, and the peaks were converted into consensus counts. Data normalization and differential comparison were performed using DESeq2. Regions of differential modification were identified for downstream analyses using a p-value cutoff of 0.05 (Wald test).
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Gastric organoids

growth_protocol: Mouse organoid cultures were established and maintained as described previously. Specifically, normal mice stomach was mechanically minced into pieces of 5-mm3 cubes and incubated in DPBS with 2.5 mM EDTA on ice. After incubation, the released gastric gland fractions were resuspended with Matrigel (Corning, Cat# 356237) and seeded in 48-wells plate. Tumor tissues were harvested and washed with ice-cold DPBS, and then minced into pieces. Incubating the minced tumor tissue in digestion medium containing 0.5 mg/ml collagenase IV (GIBCO, Cat# 17104-019) and 1.0 mg/ml collagenase I (GIBCO, Cat# 17100-017) in DMEM/F12 medium at 37°C until it dissociates into single cells or cell clusters. Tumor cells were collected by centrifugation and resuspended with Matrigel. Organoid culture medium was DMEM/F12 (GIBCO, Cat# C11330500BT) supplemented with 2 mM GlutaMAX (GIBCO, Cat# 35050-061), 1% Penicillin and Streptomycin (GIBCO, Cat# 15140-122), 1× B27 (GIBCO, Cat# A3582801), 1× N2 (GIBCO, Cat# 17502048),10 mM Y-27632, 200ng/ml FGF10 (Peprotech, Cat# 100-26-1000), 500nM A-8301 (Peprotech, Cat# 9094360), 50ng/ml mouse recombinant EGF (Peprotech, Cat# AF-100-15-1000), 100 ng/ml mouse recombinant noggin (Peprotech, Cat# 120-10C-250), 10mM Nicotinamide (Sigma, Cat# N0636), 1 mM N-acetylcysteine (Sigma, Cat# A9165), 10% Wnt3a condition medium, 10% R-spondin1 condition medium). Organoid medium was refreshed every 2-3 days.

extract_protocol: Organoids (1x105 cells/each group) were harvested in 1.5ml tubes for CUT&Tag assay using NOovoNGS CUT&Tag 3.0 High-Sensitivity Kit (Novoprotein, Cat. N259-YH01-01A). 10ul ConA beads were added into tube and incubated with cells for 10min at 25°C. The supernatant was removed and added primary antibody buffer with proper primary antibody for 2h at 25°C or overnight at 4°C. The supernatant was removed and added secondary antibody buffer for 1h at 25°C. Beads were washed for 2 times. The chromatin was combined with ChiTag TM2.0 Transposome, then fragmented using Tagmentation Buffer for 1h at 37°C. ChIP DNA was purified using DNA Clean Beads and amplified using the PCR system from this kit. PCR conditions: 72 °C for 3 min, 98 °C for 30 s, followed by 10-25 cycles of 98 °C for 15 s, 60°C for 15 s and 72 °C for 10 s, 72 °C for 2min. Amplified libraries were purified with the DNA Clean Beads.The purified ChIP DNA was used for library preparation.

value: Gastric organoids

tag: chip antibody

value: Abclonal, Cat.No.A7739


title: single cell RNAseq of organoid culture

city: Boston

first: Brian

last: Lin

state: MA

address: 136 Harrison Avenue

department: DMCB

institute: Tufts University

data_processing:
Parse split-pipe pipeline was used according to manufacturer's instructions
raw, unfiltered mtx data was imported in Scanpy for downstream processing and analysis
Assembly: MM10
Supplementary files format and content: mtx (3 file format) and processed/annotated scanpy object saved as an h5ad

source_name: Olfactory

growth_protocol: Mouse olfactory epithelium was dissected away from respiratory tissue, dissociated using papain, plated in DMEM/F12 media on tissue cultured treated plastic for 1 hour prior to collecting non-adhered cells, pelleting, and plating inside organoid culture conditions for 7 days.

extract_protocol:
Cells were dissociated from the culture well using TrypLE, resuspended as a single cell suspension before proceeding with library construction
Single cell suspension was put into the Parse single-cell RNAseq WT-Mini kit, processed according to manufacturer's instructions

value: Olfactory

value: Mixture


title: TP_antiEZH2_rep3

description: Gastric organoids, Trp53-/-;sgPten, rep3

value: Cell Signaling Technology, Cat.No.5246S


title: TPE_antiTFAP2C_rep2

description: Gastric organoids, Trp53-/-;sgPten;sgEzh2, rep2


title: TPE_antiTFAP2C_rep1

description: Gastric organoids, Trp53-/-;sgPten;sgEzh2, rep1


title: TP_antiEZH2_rep2

description: Gastric organoids, Trp53-/-;sgPten, rep2


title: TP_antiEZH2_rep1

description: Gastric organoids, Trp53-/-;sgPten, rep1


title: TPE_H3K27me3_rep1

value: Cell Signaling Technology, Cat.No.9733S


title: TPE_H3K27me3_rep2


title: TP_H3K27me3_rep2


title: TP_H3K27me3_rep1


title: Gastric tumor organoids, Trp53-/-;sgPten;sgEzh2;sgTfap2c_2, rep3

data_processing:
Transcriptome sequencing was conducted using the Illumina NovaSeq 6000 platform with 150 bp paired-end sequencing. After removing the adapters, ploy-N, and low-quality reads, clean data were aligned against the reference mouse genome (mm10) using STAR _2.6.0. Following this, raw counts were normalized and significance scores as well as log2-fold change values were calculated using the DESeq2 (v.1.22.2).
Assembly: mm10
Supplementary files format and content: csv files include counts and DESeq2 normalized data

source_name: Gastric tumor organoids

extract_protocol:
Total RNA extraction using with Trizol reagent (Thermo Fisher Scientific, Cat# 15596026) and complementary DNA (cDNA) synthetization using HiScript-III RT SuperMix kit (Vazyme, Cat# R323-01) were performed under the manufacturer’s instructions. Real-time quantitative PCR (RT-qPCR) was performed using Fast SYBR Green MasterMix (Vazyme, Cat# Q711-02/03) on the StepOne Real-Time PCR System (Thermo Fisher Scientific, Applied Biosystems QuantStudio 3).
RNA libraries for RNA-seq were prepared following manufacturer's protocols.

value: Gastric tumor organoids


title: Gastric tumor organoids, Trp53-/-;sgPten;sgEzh2;sgTfap2c_2, rep1


title: Gastric tumor organoids, Trp53-/-;sgPten;sgEzh2;sgTfap2c_2, rep2


title: TGF-β+ POG 30uM_3

first: Seokwon

last: Kim

address: 99, Daehak-ro, Yuseong-gu

institute: Chungnam National University

description: Library name: P30+TGF_P9

data_processing:
Illumina bcl2fastq (v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastp), then mapped to GRCh38 (NCBI) whole genome using STAR.
Read count extraction using HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Intestinal fibroblast

growth_protocol: Human intestinal fibroblasts (CCD-18Co, ATCC CRL-1459) and human primary intestinal fibroblasts (isolated from, Korea) were used in this study. CCD-18Co cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, USA) supplemented with 10% fetal bovine serum (FBS; Gibco) and 1% penicillin-streptomycin (Gibco) at 37°C in a humidified incubator containing 5% CO₂. Cells were used between passages 5 and 10 for all experiments.

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen).
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq V2 Library Prep Kit standard protocols.

treatment_protocol: Cells were seeded at appropriate densities and allowed to adhere overnight. To synchronize and minimize basal signaling activity, cells were serum-starved in serum-free DMEM for at least 12 hours prior to treatment initiation. Following starvation, cells were pre-treated with Prim-O-glucosylcimifugin (POG; 30 μM ; Tokyo Chemical Industry) for 4 hours. Subsequently, recombinant human TGF-β1 (2 ng/mL; PeproTech) was added to induce fibrotic signaling. For the control group, an equivalent volume of DMSO (vehicle) was added under identical conditions.

value: Intestinal fibroblast

value: fibroblast

value: Wildtype

value: CCD-18co cells were treated with TGF-β+POG30uM for 24 hours.


title: TGF-β+ POG 30uM_2

description: Library name: P30+TGF_P6


title: TGF-β_3

description: Library name: TGF_P9

value: CCD-18co cells were treated with TGF-β for 24 hours.


title: Gastric tumor organoids, Trp53-/-;sgPten;sgEzh2;sgTfap2c_1, rep3


title: TGF-β_1

description: Library name: TGF_P3


title: Control_3

description: Library name: Con_P9

value: CCD-18co cells were treated with DMSO for 24 hours.


title: TGF-β_2

description: Library name: TGF_P6


title: Gastric tumor organoids, Trp53-/-;sgPten;sgEzh2;sgTfap2c_1, rep2


title: Gastric tumor organoids, Trp53-/-;sgPten;sgEzh2;sgTfap2c_1, rep1


title: Gastric tumor organoids, Trp53-/-;sgPten;sgEzh2, rep2


title: Gastric tumor organoids, Trp53-/-;sgPten;sgEzh2, rep1


title: Gastric tumor organoids, Trp53-/-;sgPten;sgEzh2;sgScramble, rep3


title: Control_2

description: Library name: Con_P6


title: Control_1

description: Library name: Con_P3


title: Gastric tumor organoids, Trp53-/-;sgPten;sgEzh2;sgScramble, rep1


title: Gastric tumor organoids, Trp53-/-;sgPten;sgEzh2;sgScramble, rep2


title: Knock-in IkBa WT_TNF_treated_rep1

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

institute: Hospital del Mar

description: Library name: WT_T_1

data_processing:
Raw reads were trimmed to remove adapters presence with Trimgalore (v0.6.6) (Krueger et al., 2020). Default parameters were used except for a minimum quality of 15 (Phred score) and an adapter removal stringency of 3bp overlap
Trimmed reads were aligned to reference genome (hg38 release 106 from Ensembl) with STAR aligner tool (v2.7.8). STAR was executed with default parameters except for the number of allowed mismatches which was set to 1
Uniquely mapped reads were considered for further analysis. Raw gene expression was quantified using featureCounts tool from subRead software (v2.0.1) with exon as feature.
Raw counts matrix was imported into R Statistical software (v4.2.1). Prior to statistical analysis, those genes with less than 10 raw counts across the 18 samples per timepoint were discarded
For visualization purposes, counts were normalized by variance-stabilizing transformation method as implemented in DESeq2 R package (v1.38.3)
Assembly: hg38
Supplementary files format and content: Tab-separated value file: RNAseq_All_samples_Raw_counts.txt: RNAseq Raw expression levels for each gene in each individual sample as calculated using featureCounts. This data is prior to conducting any pre-filtering step.
Supplementary files format and content: Tab-separated value file: RNAseq_All_samples_Norm_counts.txt. Normalized expression levels including the expression of all genes after low filtering per all individual samples. Normalization carried out with VST from DESeq2 (v1.38.3)

growth_protocol: Cells were grown in Dulbecco’s modified Eagle’s medium (Invitrogen) plus 10% fetal bovine serum (Biological Industries) and were maintained in a 5% CO2 incubator at 37°C.

extract_protocol:
Total RNA was extracted from cells using Qiagen RNeasy Mini Kit (#74106) following manufacturer's instructions. RNA quality was measured by Nanodrop and Agarose gel
Library was prepared according to manufacturer's instructions (50bp paired-end reads)

treatment_protocol: Cells were treated with hTNFα (0,1 µg/mL) 40min.

value: Colorectal cancer cells

value: IkBa WT

value: TNF treated


title: Knock-in IkBa WT_TNF_treated_rep2

description: Library name: WT_T_2


title: Knock-in IkBa WT_TNF_treated_rep3

description: Library name: WT_T_3


title: Knock-in IkBa WT_untreated_rep3

description: Library name: WT_3

value: Untreated


title: Knock-in IkBa WT_untreated_rep2

description: Library name: WT_2


title: Gastric tumor organoids, Trp53-/-;sgPten, rep2


title: Knock-in IkBa M3_mutant_TNF_treated_rep3

description: Library name: M3_T_3

value: IkBa M3 mutant


title: Knock-in IkBa M3_mutant_TNF_treated_rep2

description: Library name: M3_T_2


title: TGF-β+ POG 30uM_1

description: Library name: P30+TGF_P3


title: Knock-in IkBa WT_untreated_rep1

description: Library name: WT_1


title: Gastric normal organoids, sgEzh2_2, rep3

source_name: Gastric normal organoids

value: Gastric normal organoids


title: Gastric normal organoids, sgEzh2_2, rep2


title: Gastric normal organoids, sgEzh2_2, rep1


title: Gastric normal organoids, sgEzh2_1, rep3


title: Knock-in IkBa M3_mutant_TNF_treated_rep1

description: Library name: M3_T_1


title: Knock-in IkBa N108_mutant_TNF_treated_rep3

description: Library name: 108_T3

value: IkBa N108 mutant


title: Gastric tumor organoids, Trp53-/-;sgPten, rep1


title: Gastric normal organoids, sgEzh2_1, rep2


title: Gastric normal organoids, sgScramble, rep2

value: sgScramble


title: Gastric normal organoids, sgEzh2_1, rep1


title: WT-MII-rep3

city: Nanjing

first: Jiashuo

last: Li

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

institute: Nanjing Medical University

data_processing:
The raw bisulfite sequencing reads were trimmed to remove adaptors and low-quality bases by using trim_galore (v0.6.10) (parameters: --quality 20 --phred33 –length 30 –stringency 3 --paired). Next, Bismark (v0.24.1) was used to map clean reads to mouse reference genome (GRCm38) with single-end alignment mode (parameters: --non_directional --bowtie2 --bam --single_end). PCR duplicates were removed using deduplicate_bismark with default parameters. And only the high-quality reads (MAPQ > 10) were retained for further analysis.
The DNA methylation level of each cytosine site in the reference genome sequence was the percentage of reads supporting C (methylated). In this study, unless specified the DNA methylation level of the CpG sites of a given sample or region represents the DNA methylation level of this sample or region. Due to low-input cells, the 1X read coverage was used to analyze the DNA methylation level.For comparison across samples, the whole genome was divided by 10-Mb consecutive windows and the average DNA methylation level of this bin was determined. Additionally, 20-Kb consecutive genomic windows were used for DNA methylation pattern analysis. The DNA methylation level of some special genomic regions were also estimated. The CGIs and repetitive regions were download from UCSC genome table. The CGI shores were defined as the regions 2-Kb around from the CGI. TSSs (transcriptional start sites), Exons, introns were extracted from gencode annotation (vM25) and the promoters were defined as the regions 2-Kb upstream from TSSs. In addition, the imprinting control regions (ICRs) were got from a previous study.Differential methylation analysis was performed using the metilene (v0.2.6) with default parameters and then the differentially methylated regions (DMRs) were annotated with ChIPseeker (v1.36.0).
Assembly: GRCm38
Supplementary files format and content: Wig including CG sites methylation values for each sample

source_name: oocyte

extract_protocol:
DNA methylome profiling.Cells were pooled into a tube with lysis buffer (10 mM Tris-HCl pH 7.4 and 2% SDS) to extract DNA. After proteinase treatment, the naked genomic DNA was subjected to bisulfite conversion (ZYMO EZ-96 DNA Methylation Kit) and then purified by Agencourt AMPure XP beads (Beckman).
DNA methylome profiling After proteinase treatment, the naked genomic DNA was subjected to bisulfite conversion (ZYMO EZ-96 DNA Methylation Kit) and then purified by Agencourt AMPure XP beads (Beckman). The converted DNA was complemented with oligo primer1 (CTACACGACGCTCTTCCGATCTNNNNNN) and 50 units of Klenow polymerase (3` to 5`exo-, NEB). The seconds were synthesized by oligo primer2 (AGACGTGTGCTCTTCCGATCTNNNNNN). Finally, the libraries were generated after 12 to 15 cycles of PCR amplification with Illumina universal PCR primer and Illumina indexed primer.

value: oocyte

value: MII

value: WT


title: Knock-in IkBa N108_mutant_untreated_rep3

description: Library name: 108_3


title: Knock-in IkBa M3_mutant_untreated_rep2

description: Library name: M3_2


title: WT-Blastocyst_rep3

source_name: blastula

value: blastula


title: WT-MII-rep1


title: WT-Blastocyst_rep2


title: Gastric normal organoids, sgScramble, rep3


title: Knock-in IkBa M3_mutant_untreated_rep1

description: Library name: M3_1


title: WT-4C-rep2

source_name: four cell

value: four cell


title: Knock-in IkBa N108_mutant_TNF_treated_rep2

description: Library name: 108_T2


title: Gastric normal organoids, sgScramble, rep1


title: Knock-in IkBa N108_mutant_TNF_treated_rep1

description: Library name: 108_T1


title: Knock-in IkBa N108_mutant_untreated_rep1

description: Library name: 108_1


title: WT-MII-rep2


title: Knock-in IkBa N108_mutant_untreated_rep2

description: Library name: 108_2


title: Flag_input_HT29

data_processing:
Raw reads were trimmed to remove adapters presence with Trimgalore (v0.6.6) (Krueger et al., 2020). Default parameters were used except for a minimum quality of 15 (Phred score) and an adapter removal stringency of 3bp overlap
Trimmed reads were aligned to reference genome (GRCh38 Ensembl release 106) with Bowtie2 (v2.4.4) which was executed with default parameters (Langmead & Salzberg, 2012). Multimapped reads and those exhibiting MAPQ < 20 were removed.
Duplicated reads were marked with SAMtools (v1.15) (Danecek et al., 2021). ENCODE blacklisted regions (hg38 v2) were removed prior to peak calling except for H3K9me3 (Amemiya et al., 2019).
BigWig files were individually generated using deepTools (v3.5.1) bamCoverage with (kept duplicates) -binSize 10 -smoothLength 30 -effectiveGenomeSize  2701495711  -normalizeUsing RPGC  and -extendReads  Fragment_Length options (Ramírez et al., 2016) where Fragment_Length was retrieved from PhantomPeakQualTools results.
Peak calling was conducted by means of MACS2 (v2.2.7.1) with -nomodel -extsize Fragment_Length -g 2701495711 -q 0.05 options (Zhang et al., 2008) where Fragment_Length was retrieved from PhantomPeakQualTools results. Corresponding input samples as control sample were used for peak calling.
Assembly: hg38
Supplementary files format and content: bigWig and narrowPeak files (except for the input samples)

growth_protocol: Cells were cultured on plastic dishes with DMEM medium + 10% FBS and 5% P/S

extract_protocol:
Cells were cross-linked by incubating them initially in Gold (Diagenode), and then they were further crosslinked in DPBS (Gibco, Cat #14190094)  supplemented with 1% formaldehyde (Sigma-Aldrich; Cat #252549) for 10 min rocking at room temperature. Cross-linking was stopped using 125 mM Glycine (Sigma-Aldrich, Cat #G8790) rocking for 5 minutes at room temperature. Cell nuclei were isolated by incubating cell pellets in a buffer containing 5mM Pipes pH 8, 85mM KCl and 0.5% NP40, and later incubated on ice for 10 minutes followed by centrifuge at 4000 rpm for 5 minutes at 4ºC. Nucleus were lysed in a buffer containing 1% SDS, 10mM EDTA and 50 mM Tris-HCl pH 8.1 and incubated on ice for 10 min. Samples were sonicated 25 cycles (30´´on/30´´off)  and SDS was removed by incubating the sonicated sample on ice for 1 hour and later centrifuged for 15 at 4ºC and 16000g. 60μg of chromatin was incubated with 10 μg of ANTI-FLAG® M2 (Sigma-Aldrich, Cat #F1804). Samples were pulled down by a 50/50 mix of Dynabeads A (Invitrogen, Cat #10002D) and G (Invitrogen, Cat #10003D). Samples were washed 4 times in 0.1% SDS, 1% Triton-X, 2mM EDTA, 20mM Tris-HCl pH 8 and 150mM NaCl; followed by 1 wash in TE pH 8.  Samples were then eluted in 1% SDS and 100mM NaHCO3. Samples were descrosslinked by incubating for 16 hours (or overnight) at 65ºC shaking at 450 rpm, and were treated with Proteinase K for 1h at 45ºC. DNA was purified using QIAquick PCR Purification Kit (Qiagen, Cat #28106), following the manufacturer’s instructions.
Libraries prepared according to manufacturer's instructions (SE 50bp reads)

value: wildtype

value: none (input)


title: IkBa_Flag_HT29_rep2

value: Monoclonal ANTI-FLAG®M2 antibody (#F1804, Sigma)


title: WT-Blastocyst_rep1


title: IkBa_Flag_HT29_rep3


title: IkBa_Flag_HCT116_rep3


title: IkBa_Flag_HT29_rep1


title: Flag_input_HCT116


title: Knock-in IkBa M3_mutant_untreated_rep3

description: Library name: M3_3


title: IkBa_Flag_HCT116_rep1


title: Ftdc2_KO_MII_rep1


title: Ftdc2_KO_Blastocyst_rep1


title: Ftdc2_KO_Blastocyst_rep3


title: Ftdc2_KO_MII_rep3


title: soybeans m6A-IP, mature seed, Rep.1

city: beijing

first: li

last: yaping

address: 中关村南大街12号

institute: 中国农业科学院生物所

description: A14_1 m6A-IP

data_processing:
The raw reads were trimmed using TrimGalore-0.6.10
The trimmed reads were aligned to the GCA_021733175.1_JD17 reference genome using Hisat2(2.1.0)
Expression levels were estimated using featureCounts (v2.0.6)
Peak calling was performed using MACS2 (2.2.8)
etc.
Assembly: GCA_021733175.1_JD17
Supplementary files format and content: csv files include TPM values for each Sample

organism: Glycine max

source_name: mature seed

extract_protocol:
The total RNA was extracted using Eastep Super Total RNA Extraction Kit(Promega) following the manufacturer’s procedure.
m6A-seq2 was performed as Dierks et al., 2021. The input was used as RNA-Seq&Input.

value: mature seed

value: tissue

value: SoyC11 soybeans,WT

value: Planting in the field


title: soybeans m6A-IP, mature seed, Rep.2

description: A14_2 m6A-IP


title: Ftdc2_KO_Blastocyst_rep2


title: WT-4C-rep1


title: Ftdc1_KO_MII_rep3


title: Ftdc2_KO_4C_rep2


title: Ftdc2_KO_4C_rep1


title: soybeans m6A-IP, green seed, Rep.3

description: A13_3 m6A-IP

source_name: green seed

value: green seed


title: Ftdc1_KO_MII_rep2


title: soybeans m6A-IP, green seed, Rep.2

description: A13_2 m6A-IP


title: soybeans m6A-IP, green seed, Rep.1

description: A13_1 m6A-IP


title: Ftdc1_KO_MII_rep1


title: soybeans m6A-IP, root nodule at R5 stage, Rep.2

description: A12_2 m6A-IP

source_name: root nodule

value: root nodule


title: Ftdc1_KO_Blastocyst_rep3


title: Ftdc2_KO_MII_rep2


title: IkBa_Flag_HCT116_rep2

value: Colorectal cancer cells


title: soybeans m6A-IP, root nodule at R5 stage, Rep.3

description: A12_3 m6A-IP


title: Ftdc1_KO_Blastocyst_rep1


title: Ftdc1_KO_Blastocyst_rep2


title: soybeans m6A-IP, pod at R6 stage, Rep.3

description: A11_3 m6A-IP

source_name: pod

value: pod


title: soybeans m6A-IP, mature seed, Rep.3

description: A14_3 m6A-IP


title: soybeans m6A-IP, pod at R6 stage, Rep.2

description: A11_2 m6A-IP


title: Ftdc1_KO_4C_rep1


title: soybeans m6A-IP, root nodule at R5 stage, Rep.1

description: A12_1 m6A-IP


title: Ftdc1_KO_4C_rep2


title: soybeans m6A-IP, root at R5 stage, Rep.3

description: A10_3 m6A-IP

source_name: root

value: root


title: Dnmt1_KO_MII_rep3

value: oocyte


title: Dnmt1_KO_MII_rep1

value: MII


title: soybeans m6A-IP, root at R5 stage, Rep.2

description: A10_2 m6A-IP


title: Dnmt1_KO_MII_rep2


title: soybeans m6A-IP, root at R5 stage, Rep.1

description: A10_1 m6A-IP


title: soybeans m6A-IP, flower, Rep.3

description: A9_3 m6A-IP

source_name: flower

value: flower


title: Dnmt1_KO_Blastocyst_rep3

value: blastula


title: Dnmt1_KO_Blastocyst_rep1


title: soybeans m6A-IP, flower, Rep.2

description: A9_2 m6A-IP


title: Dnmt1_KO_Blastocyst_rep2


title: Dnmt1_KO_4C_rep1

value: four cell


title: soybeans m6A-IP, trifoliolate leaf at V1 stage, Rep.2

description: A8_2 m6A-IP

source_name: trifoliolate leaf

value: trifoliolate leaf

value: 25℃, light/dark=14h/10h


title: soybeans m6A-IP, flower, Rep.1

description: A9_1 m6A-IP


title: soybeans m6A-IP, trifoliolate leaf at V1 stage, Rep.1

description: A8_1 m6A-IP


title: WT-Blasto-1

data_processing:
For RNA-seq data, adaptors and low-quality bases were removed with trim_galore (v0.6.10) and sequences were mapped to mouse reference genome (GRCm38) using HISAT2 (v2.2.0) with gencode annotation (vM25). Read quantification was carried out with FeatureCounts (v2.0.6) (parameters: -t exon -g gene_id -Q 10 --primary -s 0 -p).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
The zona pellucidae of oocytes and blastocysts were removed with 0.5% pronase E (Sigma). 14 oocytes per sample (2 samples for each group) and 5 blastocysts per sample ( 2 samples for each group) were lysed and subjected to first strand synthesis.
The single-strand RNA molecules were reversed with oligo (dT) primer. Amplified cDNA was fragmented into ~300 bp fragments and then constructed by TruePrep DNA Library Prep Kit (Vazyme).

value: WT


title: NE.KO.F77-1

description: gene expression data from adult Tatd knockout mouse

source_name: brain cortex tatd-/- female

value: female

value: tatd-/-

value: brain cortex

value: Adult (2 months)


title: ftdc2_wt_m2_re2


title: ftdc2_wt_m2_re1


title: soybeans m6A-IP, cotyledon at V1 stage, Rep.1

description: A7_1 m6A-IP

source_name: seedling cotyledon

value: seedling cotyledon

value: tissue

value: SoyC11 soybeans,WT


title: soybeans m6A-IP, pod at R6 stage, Rep.1

description: A11_1 m6A-IP

value: pod

value: Planting in the field


title: soybeans m6A-IP, cotyledon at V1 stage, Rep.2

description: A7_2 m6A-IP


title: ftdc2_wt_gv_re3

value: oocyte

value: GV


title: soybeans m6A-IP, root at V1 stage, Rep.3

description: A6_3 m6A-IP

source_name: seedling root

value: seedling root


title: ftdc2_wt_gv_re1


title: soybeans m6A-IP, root at V1 stage, Rep.2

description: A6_2 m6A-IP


title: soybeans m6A-IP, root at V1 stage, Rep.1

description: A6_1 m6A-IP


title: ftdc2_ko_m2_re2

value: MII


title: soybeans m6A-IP, stem at V1 stage, Rep.2

description: A5_2 m6A-IP

source_name: seedling stem

value: seedling stem


title: ftdc2_ko_gv_re2


title: ftdc2_ko_m2_re1


title: soybeans m6A-IP, trifoliolate leaf at V1 stage, Rep.3

description: A8_3 m6A-IP

value: trifoliolate leaf


title: Dnmt1_KO_4C_rep2

value: four cell


title: ftdc2_ko_gv_re1


title: WT-Blasto-2

value: blastula

value: WT


title: soybeans m6A-IP, stem at V1 stage, Rep.1

description: A5_1 m6A-IP

value: 25℃, light/dark=14h/10h


title: Ft2-Blasto-2


title: soybeans m6A-IP, unifoliolate leaf at V1 stage, Rep.3

description: A4_3 m6A-IP

source_name: unifoliolate leaf

value: unifoliolate leaf


title: Ft1-Blasto-4


title: Ft2-Blasto-1


title: soybeans m6A-IP, unifoliolate leaf at V1 stage, Rep.1

description: A4_1 m6A-IP


title: soybeans m6A-IP, unifoliolate leaf at V1 stage, Rep.2

description: A4_2 m6A-IP


title: soybeans m6A-IP, cotyledon at V1 stage, Rep.3

description: A7_3 m6A-IP


title: Ft1-Blasto-3


title: soybeans m6A-IP,  root  at VE stage, Rep.3

description: A3_3 m6A-IP

source_name: tender root

value: tender root

value: 25℃, light/dark=14h/10h,  sterilized water for 7 days


title: soybeans m6A-IP,  root  at VE stage, Rep.2

description: A3_2 m6A-IP

value: tissue


title: soybeans m6A-IP,  root  at VE stage, Rep.1

description: A3_1 m6A-IP

value: SoyC11 soybeans,WT


title: Dt1-Blasto-3


title: soybeans m6A-IP, cotyledon Rep.3

description: A2_3 m6A-IP

source_name: cotyledon

value: cotyledon

value: 25℃, light/dark=14h/10h,  sterilized water for 5 days


title: Dt1-Blasto-4


title: SCW-9M-2

data_processing:
Reads were processed using the Cell Ranger 7.1.0 pipeline with default and recommended parameters. FASTQs generated from Illumina sequencing output were aligned to the mouse genome, version GRCm38, using the STAR algorithm. Next, Gene-Barcode matrices were generated for each individual sample by counting UMIs and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: ovary

extract_protocol:
Tissues were transported in In sterile culture dish with 10 ml 1x Dulbecco's Phosphate-Buffered Saline (DPBS; Thermo Fisher, Cat. no. 14190144) on ice to remove the residual tissue storage solution, then minced on ice. We used dissociation enzyme 0.25% Trypsin (Thermo Fisher, Cat. no. 25200-072) and 10 ug/mL lDNase I (Sigma, Cat. no. 11284932001) dissolved in PBS with 5% Fetal Bovine Serum (FBS; Thermo Fisher, Cat. no. SV30087.02) to digest the tissues. XX tissues were dissociated at 37 ℃ with a shaking speed of 50 r.p.m for about 40 min.We repeatedly collected the dissociated cells at interval of 20 min to increase cell yield and viability. Cell suspensions were filtered using a 40 um nylon cell strainer and red blood cells were removed by 1X Red Blood Cell Lysis Solution (Thermo Fisher, Cat. no. 00-4333-57) . Dissociated cells were washed with 1x DPBS containing 2% FBS. Cells were stained with 0.4% Trypan blue (Thermo Fisher, Cat. no. 14190144) to check the viability on Countess® II Automated Cell Counter (Thermo Fisher).
Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a Gel Beads-in-emulsion(GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification.Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (Chromium Single Cell 3ʹ v3). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.

value: ovary

value: female

tag: strain

value: white brown rice


title: soybeans m6A-IP, stem at V1 stage, Rep.3

description: A5_3 m6A-IP


title: SCW-9M-1


title: soybeans m6A-IP, imbibition seed Rep.3

description: A1_3 m6A-IP

source_name: imbibition seed

value: imbibition seed

value: 25℃, light/dark=14h/10h,  sterilized water for 1 days


title: SCP-9M-1

value: polish rice


title: soybeans m6A-IP, cotyledon Rep.2

description: A2_2 m6A-IP


title: SCB-9M-3

value: black rice


title: soybeans m6A-IP, imbibition seed Rep.2

description: A1_2 m6A-IP


title: soybeans m6A-IP, imbibition seed Rep.1

description: A1_1 m6A-IP


title: SCW-9M-3


title: SCB-9M-2


title: soybeans Input, mature seed, Rep.2

description: A14_2 Input

value: mature seed

value: Planting in the field


title: soybeans m6A-IP, cotyledon Rep.1

description: A2_1 m6A-IP


title: SCB-9M-1


title: SCP-9M-3


title: SCW-6M-3


title: soybeans Input, green seed, Rep.2

description: A13_2 Input

value: green seed


title: SCW-6M-1


title: soybeans Input, mature seed, Rep.1

description: A14_1 Input


title: SCW-6M-2


title: soybeans Input, root nodule at R5 stage, Rep.3

description: A12_3 Input

value: root nodule


title: SCP-6M-2


title: soybeans Input, green seed, Rep.3

description: A13_3 Input


title: soybeans Input, green seed, Rep.1

description: A13_1 Input


title: SCP-6M-3


title: SCP-6M-1


title: soybeans Input, root nodule at R5 stage, Rep.1

description: A12_1 Input


title: SCB-6M-2


title: soybeans Input, pod at R6 stage, Rep.3

description: A11_3 Input

value: pod


title: SCB-6M-1


title: soybeans Input, mature seed, Rep.3

description: A14_3 Input


title: soybeans Input, pod at R6 stage, Rep.2

description: A11_2 Input


title: soybeans Input, pod at R6 stage, Rep.1

description: A11_1 Input


title: CM_rep3

city: Brookline

first: Swathy

last: Babu

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana Farber Cancer Institute

data_processing:
Identify open chromatin regions of interest: Mapping was done with Bowtie v1.2.2: single-end mode with parameters -k 1 -m 1 –best and -l set to read length. Peaks were called useing MACS v1.4.1 using parameters -p 1e-9. Peaks were collapsed across all samples using bedtools merge. Collapsed peaks were assigned to the RefSeq gene with the single most proximal transcription start site using bedtools closest.
Quantify open chromatin regions of interest:
Read trimming: Cutadapt, parameters –minimum-length 25 -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT.
Read alignment: Bowtie v1.2.2, paired-end mode, parameters --allow-contain --maxins=100000 --chunkmbs=256 -k 1 -m 1 –best.
Counting and differential expression: Fragments were generated from paired-end mappings using samtools view, samtools sort, bedtools bamtobed, and bedtools bedtobam. These fragments were used to calculate coverage of collapsed peaks defined above using bedtools intersect -c. Fragment counts in each collapsed region were used as input for DEseq2 with default parameters to compare the cutaneous and mucosal region coverage.
Data visualization: Genome-wide coverage in 50bp bins was quantified using bedtools intersect -c, normalized to the number of mapped reads per sample, and converted to TDF with igvtools.
Assembly: danRer11
Supplementary files format and content: .xls file contains differential chromatin accessibility of mucosal melanoma samples vs. cutaneous melanoma

organism: Danio rerio

source_name: cutaneous melanoma

growth_protocol: Melanomas generated from roy-/-; mitfa-/- zebrafish injected with CRISPR MCR:tp53 sgRNA; CRISPR MCR:ptena/b sgRNA; MCR:CCND1 or mitfa-/-; tp53-/-; BRAFV600E; crestin:EGFP zebrafish injected with MCR empty.

extract_protocol:
Tumors were harvested, cell suspensions were made, and cells were were lysed and subjected to tagmentation reactions per instructions (Nextera 15028212).
Nextera 15028212

value: cutaneous melanoma

value: melanoma

value: mitfa-/-; tp53-/-; BRAFV600E; crestin:EGFP fish injected with MCR:Empty, mitfa:mCherry, Tyrosinase gRNA and Cas9


title: soybeans Input, root at R5 stage, Rep.2

description: A10_2 Input

value: root

value: tissue

value: SoyC11 soybeans,WT


title: soybeans Input, root at R5 stage, Rep.3

description: A10_3 Input


title: CM_rep1


title: Asexual Schizont-stage bisulfite treated tRNA, biol rep3

city: Stockholm

first: Sherwin

last: Chan

address: Solnavagen 9

country: Sweden

institute: Karolinska Institutet

description:
Library name: Bisulfite_S3
fastq files from four lanes of the same flow cells were concatenated into one fastq file

library_source: other

data_processing:
Basecalls were performed using Generate FASTQ v 2.0.1 for NextSeq output
UMI was extracted using UMI_tools v1.1.2.  Sequence reads were trimmed for adaptor sequence using fastx_toolkit v0.0.14
Trimmed reads were mapped to the reference using Bowtie2 v2.2.1 with sensitive local mode
UMI  deduplication was performed using UMI_tools v1.1.2. Read counts were then extracted from htseq-count v0.9.1
Assembly: In-house curated tRNA reference including both Plasmodium falciparum and homo sapiens tRNA sequences
Supplementary files format and content: tab-delimited text files (tabular) of raw count for each Sample

molecule: other

organism: Plasmodium falciparum

growth_protocol: infected red blooc cells were grown in RPMI 1640 supplemented with 10% pooled human serum, cultured at 37C at 5% CO2, 5% O2

extract_protocol:
MirVana miRNA isolation kit (invitrogen), small RNA purification according to manufacturer's instruction, for periodate treatment, the RNA was treated in 100 mM NaOAc/HOAc, pH 4.8 and freshly prepared 50 mM NaIO4 at room temperature for 30 mins and then column purified. The recovered RNA was treated again in 60 mM sodium borate, pH 9.5 at 45°C for 90 min before final column purification
library was constructed using TGIRT3 modular kit (InGex), 100ng small RNA was used as input, RNA-Seq, single-end 120 cycles

value: Infected red blood cell

value: complete medium


title: soybeans Input, root at R5 stage, Rep.1

description: A10_1 Input


title: Asexual Trophozoite-stage bisulfite treated tRNA, biol rep3

description:
Library name: Bisulfite_T3
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: soybeans Input, flower, Rep.3

description: A9_3 Input

value: flower


title: Asexual ring-stage bisulfite treated tRNA, biol rep3

description:
Library name: Bisulfite_R3
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: Asexual Schizont-stage bisulfite treated tRNA, biol rep2

description:
Library name: Bisulfite_S2
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: soybeans Input, root nodule at R5 stage, Rep.2

description: A12_2 Input


title: SCB-6M-3

value: ovary

value: female


title: soybeans Input, trifoliolate leaf at V1 stage, Rep.3

description: A8_3 Input

value: trifoliolate leaf

value: 25℃, light/dark=14h/10h


title: Asexual ring-stage bisulfite treated tRNA, biol rep2

description:
Library name: Bisulfite_R2
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: soybeans Input, trifoliolate leaf at V1 stage, Rep.2

description: A8_2 Input


title: soybeans Input, trifoliolate leaf at V1 stage, Rep.1

description: A8_1 Input


title: soybeans Input, cotyledon at V1 stage, Rep.3

description: A7_3 Input

value: seedling cotyledon


title: soybeans Input, cotyledon at V1 stage, Rep.2

description: A7_2 Input


title: Asexual Trophozoite-stage bisulfite treated tRNA, biol rep1

description:
Library name: Bisulfite_T1
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: soybeans Input, cotyledon at V1 stage, Rep.1

description: A7_1 Input


title: Asexual ring-stage bisulfite treated tRNA, biol rep1

description:
Library name: Bisulfite_R1
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: CM_rep2


title: 143b_HS-ICTO+US-3

city: Chengdu

first: Xiao

last: Rong

state: None Selected

address: Guoxuexiang 37

institute: West China Hospital, Sichuan University

description: Library name: Sample9

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

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

value: osteosarcoma cell

value: WT

value: Co-culture with HS-ICTO scaffold and US applied


title: 143b_HS-ICTO+US-2

description: Library name: Sample8


title: soybeans Input, root at V1 stage, Rep.3

description: A6_3 Input

value: seedling root


title: soybeans Input, root at V1 stage, Rep.1

description: A6_1 Input


title: soybeans Input, flower, Rep.2

description: A9_2 Input

value: Planting in the field


title: 143b_HS-ICTO+US-1

description: Library name: Sample7


title: soybeans Input, stem at V1 stage, Rep.3

description: A5_3 Input

value: seedling stem


title: ring-stage cutlure, treated with 10nM DHA, biol rep2

description:
Library name: 10nM-DHA-R2
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: 143b_HS-ICTO-3

description: Library name: Sample6

value: Co-culture with HS-ICTO scaffold


title: 143b_HS-ICTO-2

description: Library name: Sample5


title: soybeans Input, stem at V1 stage, Rep.2

description: A5_2 Input

value: tissue


title: ring-stage cutlure, no DHA treatment control, biol rep2

description:
Library name: DHA-control_2
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: soybeans Input, flower, Rep.1

description: A9_1 Input

value: SoyC11 soybeans,WT


title: soybeans Input, stem at V1 stage, Rep.1

description: A5_1 Input


title: soybeans Input, unifoliolate leaf at V1 stage, Rep.3

description: A4_3 Input

value: unifoliolate leaf


title: Asexual Trophozoite-stage bisulfite treated tRNA, biol rep2

description:
Library name: Bisulfite_T2
fastq files from four lanes of the same flow cells were concatenated into one fastq file

value: Infected red blood cell

value: complete medium


title: ring-stage cutlure, treated with 700nM DHA, biol rep1

description:
Library name: 700nM-DHA-R1
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: 143b_HS-ICTO-1

description: Library name: Sample4


title: Asexual Schizont-stage bisulfite treated tRNA, biol rep1

description:
Library name: Bisulfite_S1
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: soybeans Input, unifoliolate leaf at V1 stage, Rep.2

description: A4_2 Input


title: ring-stage cutlure, treated with 10nM DHA, biol rep1

description:
Library name: 10nM-DHA-R1
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: soybeans Input, unifoliolate leaf at V1 stage, Rep.1

description: A4_1 Input


title: soybeans Input,  root  at VE stage, Rep.3

description: A3_3 Input

value: tender root

value: 25℃, light/dark=14h/10h,  sterilized water for 7 days


title: soybeans Input,  root  at VE stage, Rep.2

description: A3_2 Input


title: 143b_HS-3

description: Library name: Sample3

value: Co-culture with HS scaffold


title: soybeans Input,  root  at VE stage, Rep.1

description: A3_1 Input


title: soybeans Input, root at V1 stage, Rep.2

description: A6_2 Input

value: 25℃, light/dark=14h/10h


title: ring-stage cutlure, treated with 700nM DHA, biol rep2

description:
Library name: 700nM-DHA-R2
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: 143b_HS-2

description: Library name: Sample2


title: soybeans Input, cotyledon Rep.2

description: A2_2 Input

value: cotyledon

value: 25℃, light/dark=14h/10h,  sterilized water for 5 days


title: m3C32 knock-out Ring-stage culture, biol rep3

description:
Library name: m3C32_KO_R3
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: soybeans Input, cotyledon Rep.1

description: A2_1 Input


title: soybeans Input, cotyledon Rep.3

description: A2_3 Input


title: m3C32 knock-out Ring-stage culture, biol rep2

description:
Library name: m3C32_KO_R2
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: ring-stage cutlure, no DHA treatment control, biol rep1

description:
Library name: DHA-control_1
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: soybeans Input, imbibition seed Rep.3

description: A1_3 Input

value: imbibition seed

value: 25℃, light/dark=14h/10h,  sterilized water for 1 days


title: m3C32 knock-out Ring-stage culture, biol rep1

description:
Library name: m3C32_KO_R1
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: soybeans Input, imbibition seed Rep.2

description: A1_2 Input


title: THP-1 Cells,shCYTH4,1

city: ganzhou

first: qiu

last: xiaofen

address: No. 16, Meiguan Avenue

institute: ganzhou People's Hospital

description: Library name: Sample10

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

source_name: Bone marrow

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

value: Bone marrow

value: Acute Myeloid Leukemia

value: CYTH4 knockdown


title: THP-1 Cells,shCYTH4,3

description: Library name: Sample12


title: AlkB demethylase treatment, biol rep2

description:
Library name: demethylase_treatment2
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: THP-1 Cells,shCYTH4,2

description: Library name: Sample11


title: soybeans Input, imbibition seed Rep.1

description: A1_1 Input


title: AlkB demethylase no treatment control, biol rep2

description:
Library name: demethylase_control2
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: THP-1 Cells,shControl,3

description: Library name: Sample9

value: shControl


title: pt1333_M127_4, scRNAseq

description: 10x Genomics

data_processing:
Cell Ranger (v3.1) was used to perform sample demultiplexing, barcode processing, alignment, filtering, and UMI counting.
Assembly: hg19
Supplementary files format and content: Tab-separated values files, matrix files, and h5 files that include Cell Ranger processed data

source_name: vulva

extract_protocol:
Patient mucosal melanoma samples were disassociated, frozen, then thawed for library preparation.
10x genomics

value: vulva

tag: disease

value: mucosal melanoma


title: AlkB demethylase treatment, biol rep1

description:
Library name: demethylase_treatment1
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: THP-1 Cells,shControl,2

description: Library name: Sample8


title: AlkB demethylase no treatment control, biol rep1

description:
Library name: demethylase_control1
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: THP-1 Cells,shControl,1

description: Library name: Sample7


title: pt1333_M127_2, scRNAseq

description: 10x Genomics


title: Gametocyte induction_Day 7, biol rep3

description:
Library name: R3-DAY7
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: MV4-11 cells,shCYTH4,3

description: Library name: Sample6


title: pt1333_M127_1, scRNAseq

description: 10x Genomics


title: MV4-11 cells,shCYTH4,2

description: Library name: Sample5


title: 143b_HS-1

description: Library name: Sample1

value: osteosarcoma cell

value: WT


title: Gametocyte induction_Day 5, biol rep3

description:
Library name: R3-DAY5
fastq files from four lanes of the same flow cells were concatenated into one fastq file

value: Infected red blood cell

value: complete medium


title: Gametocyte induction_Day 3, biol rep3

description:
Library name: R3-DAY3
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: MV4-11 cells,shCYTH4,1

description: Library name: Sample4


title: Gametocyte induction_Day 1, biol rep3

description:
Library name: R3-DAY1
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: MV4-11 cells,shControl,3

description: Library name: Sample3


title: Plate 5B, Untreated, DMSO, Drugs, Replicate Plate 5A

city: New York

first: Lorenzo

last: Tomassoni

address: 1130 St Nicholas Avenue

institute: Columbia University

description: De-multiplexed Gene Expression Values for each well and the corresponding metadata are provided in the two supplementary files

data_processing:
The reads in each FASTq file, in which cDNS of 96-well samples were pooled together, were demultiplexed using a computational tool called Sabre (https://github.com/najoshi/sabre/), using the plate barcode identifiers. Then, we applied kallisto to quantify read counts and gene expression abundance matrices (e.g. transcripts per million; TPM) for each well in each plate. Specifically, we first generated human transcriptome indexes from the human genome reference (Homo_sapiens.GRCh38.cdna.all.fa and Homo_sapiens.GRCh38.96.gtf as of Mar/12/2019) in Ensembl, using 'kallisto index'. Then, the transcriptome indexes were used during 'kallisto quant' to quantify pair-end reads of the PLATE-seq data
Assembly: GRCh38
Supplementary files format and content: Tab-separated tpm values of each gene (rows) in each well (columns ) (tpm-plateseq_geoSubmission.tsv)
Supplementary files format and content: Metadata with all the details of each well (meta-plateseq_geoSubmission.tsv.tsv)
Library strategy: Plate-Seq

source_name: Human Ariway Epithelium

growth_protocol: tracheal basal cells isolated from a de-identified human lung specimen was expanded in PneumaCULT-Ex expansion media (StemCell Technologies, MA) and seeded on collagen-coated 96-well transwells. Once the cells reached confluence, media in the upper chamber of the transwell was removed and the media in the bottom chamber will be changed to PneumaCULT-ALI media (StemCell Technologies, MA) containing compounds including retinoic acid to induce cell differentiation. Differentiation efficiency on ALI day 21 was evaluated by measuring markers for ciliated cell (FOXJ1, ac-Tubulin), secretory cell (MUC5AC, CC10), and basal cells (TP63, KRT5) using immunofluorescence analysis.

extract_protocol:
Cell lysis buffer was be added to each well for RNA isolation at ALI day 21. Lysed cell suspension was first transferred to an oligo-coated plate for mRNA capturing then to a new plate for reverse transcription where barcoded oligos were used. Barcoded cDNA was  combined into one single tube and be prepared for bulk RNA-seq. Triplicate wells were used for each drug to control variation.
A library of 441 unique FDA-approved compounds (selleckchem.com)  in 10 Mm DMSO were used.

treatment_protocol: Candidate drugs from selected library were added at Cmax to epithelial cells at day 21 of ALI culture for 24 hours.

value: Human Ariway Epithelium

value: Untreated (4 Wells) - DMSO (4 Wells) - Dugs (88 Wells)


title: Gametocyte induction_Day -1, biol rep3

description:
Library name: R3-DAY-1
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: MM_rep3 [RNA-Seq]

data_processing:
Cutadpt was used to remove adaptor sequences and low quality regions.
The high-quality reads were aligned to UCSC build danRer11 of zebrafish genome using Tophat 2.0.11 without novel splicing form calls.
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1.
Assembly: danRer11
Supplementary files format and content: .txt file contains differential gene expression of mucosal melanoma samples vs. cutaneous melanoma

source_name: mucosal melanoma

growth_protocol: Melanomas generated from mitfa-/-; tp53-/-; BRAFV600E zebrafish injected with MCR:EGFP or roy-/-; mitfa-/- zebrafish injected with CRISPR MCR:tp53 sgRNA; CRISPR MCR:ptena/b sgRNA; MCR:CCND1were isolated for RNA-seq.

extract_protocol:
Tissue was disrupted using QIAshredder columns (Qiagen 79656). DNA was removed and RNA was purified using columns (Qiagen 74134). RNA was polyA selected (NEB E7490).
NEBNext Ultra RNA Library Prep Kit for Illumina (NEB E7530)

value: melanoma

value: roy-/-; mitfa-/- fish injected with CRISPR MCR:tp53 sgRNA; CRISPR MCR:ptena/b sgRNA; MCR:CCND1


title: MV4-11 cells,shControl,2

description: Library name: Sample2


title: Gametocyte induction_Day 7, biol rep2

description:
Library name: R2-DAY7
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: Plate 5A, Untreated, DMSO, Drugs


title: pt1333_M127_3, scRNAseq

description: 10x Genomics


title: MM_rep5 [RNA-Seq]


title: Plate 6B, Untreated, DMSO, Drugs, Replicate Plate 6A

value: Untreated (3 Wells) - DMSO (4 Wells) - Dugs (89 Wells)


title: Plate 6A, Untreated, DMSO, Drugs


title: Plate 4B, Untreated, DMSO, Drugs, Replicate Plate 4A


title: MV4-11 cells,shControl,1

description: Library name: Sample1


title: MM_rep1 [RNA-Seq]


title: MIA PaCa-2, STN1, CUT&Tag

city: Beijing

first: Chengqi

last: Yi

address: Yiheyuan Road

department: School of Life Sciences

institute: Peking University

description: Library name: STN1

data_processing:
Adaptor and low-quality reads were trimmed using cutadapt
FastQC was used for quality control of the sequencing data.
Reads were aligned to the human (GRCh38) reference genome using bowtie2
Only uniquely mapped reads with mapping quality > 30 were kept, normalized (to reads per million, rpm) and reformatted in te bigWig file format.
Assembly: GRCh38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: MIA PaCa-2

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicilli/strptomycin. Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
Indicated cells were digested into singles cells and respended in PBS. 10,000 cells were used, collected by magnetic beads and incubated with primary antibody, secomdary antibody and pA/G-Tn5 according to the protocol of TranNGS CUT&Tag Library Prep Kit for Illumina by Transgenebiotech.
CUT&Tag libraries were prepared using TranNGS CUT&Tag Library Prep Kit for Illumina by Transgenebiotech and constructed by PCR amplification. The number of amplification cycles is 11.

value: MIA PaCa-2

value: human pancreatic cancer cell lines


title: Plate 4A, Untreated, DMSO, Drugs


title: Gametocyte induction_Day 5, biol rep2

description:
Library name: R2-DAY5
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: CM_rep3 [RNA-Seq]

value: cutaneous melanoma

value: mitfa-/-; tp53-/-; BRAFV600E fish injected with MCR:EGFP


title: MIA PaCa-2, STAT3, CUT&Tag

description: Library name: STAT3


title: Plate 2B, Untreated, DMSO, Drugs, Replicate Plate 2A


title: CM_rep2 [RNA-Seq]


title: Gametocyte induction_Day 3, biol rep2

description:
Library name: R2-DAY3
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: Plate 2A, Untreated, DMSO, Drugs


title: MIA PaCa-2, IgG, CUT&Tag

description: Library name: IgG


title: MM_rep4 [RNA-Seq]


title: CM_rep1 [RNA-Seq]


title: pt85_107_6, scRNAseq

description: 10x Genomics

source_name: anus

value: anus


title: MM_rep2 [RNA-Seq]


title: Plate 1B, Untreated, DMSO, Drugs, Replicate Plate 1A


title: Gametocyte induction_trophozoite control, biol rep3

description:
Library name: R3-Trophozoite_induction
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: Gametocyte induction_trophozoite control, biol rep2

description:
Library name: R2-Trophozoite_induction
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: pt78_107_5, scRNAseq

description: 10x Genomics

source_name: right femoral lymph node

value: right femoral lymph node


title: MM_rep3


title: Gametocyte induction_Day 7, biol rep1

description:
Library name: R1-DAY7
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: Gametocyte induction_Day 5, biol rep1

description:
Library name: R1-DAY5
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: Doxy-treated IκBα WT  rep2

description:
WT_D2
RNAseq_INDs_ikBa_gene_quantification.txt (col. 18)

data_processing:
Basecalls performed using CASAVA version 1.4
FastQC software was used to summarize the quality of the sequenced reads. Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped toGrCh38 whole genome using STAR with default parameters except for the number of allowed mismatches which was set to 1.
Obtained BAM files with uniquely mapped reads were considered for further analysis. Raw gene expression was quantified using featureCounts tool from subRead software
DESeq2 R package was run to infer differentially expressed genes accross samples. Comparisons between treatment conditions per cell type were considered
Assembly: GRCh38
Supplementary files format and content: txt file generated from featureCounts containing all samples counts in separate columns

source_name: Doxy-treated HT29 IκBα WT rep2

growth_protocol: Starting material was freshly cells from HT29 WT, HT29 N108A mutant and HT29 triple mutant which were treated with 0.067 ug/mL, 0.04 ug/mlL and 1 ug/mL with doxycicline for 16h, respectively.

extract_protocol:
Direct RNA isolation with RNeasy Mini Kit (Qiagen Cat. No. 74106)
Samples were processed to obtain cDNA following manufacture’s protocol. cDNA amplification was performed by Long Distance PCR (LD-PCR) and the PCR-amplified cDNA purified by immobilization on AMPure XP beads (Agencourt AMPure XP kit). Samples were analyzed with Agilent High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626). Covaris shearing was used for Illumina Low input sample preparation and Double last bead purification was performed to remove fragments below 200 bp. Next, samples were used to generate an Illumina sequencing library by NEBNext Ultra protocol following kit instructions. After PCR amplification of the library, the quality was checked on a Bioanalyzer and total cDNA was sequenced using an Illumina NextSeq500 sequencer.

tag: cells

tag: origin

value: IκBalpha WT

tag: phenotype

value: doxycicline inducible

value: human colorectal adenocarcinoma


title: MM_rep2

value: mucosal melanoma

tag: cell type


title: Gametocyte induction_Day 3, biol rep1

description:
Library name: R1-DAY3
fastq files from four lanes of the same flow cells were concatenated into one fastq file

value: Infected red blood cell


title: pt86_107_4, scRNAseq

description: 10x Genomics

source_name: distal ileum and cecum

value: distal ileum and cecum


title: Plate 1A, Untreated, DMSO, Drugs

value: Human Ariway Epithelium


title: Doxy-treated IκBα WT  rep1

description:
WT_D1
RNAseq_INDs_ikBa_gene_quantification.txt (col. 17)

source_name: Doxy-treated HT29 IκBα WT rep1


title: pt55_107_2, scRNAseq

description: 10x Genomics

source_name: right axillar lymph node

value: right axillar lymph node


title: MM_rep1

value: melanoma


title: Untreated IκBα WT  rep2

description:
WT_CT2
RNAseq_INDs_ikBa_gene_quantification.txt (col. 16)

source_name: Untreated HT29 IκBα WT rep2

value: untreated


title: rat_HS-ICTO-3

description: Library name: Sample15

organism: Rattus norvegicus

source_name: Bone

value: Bone

value: WT

value: Implanted with HS-ICTO scaffold


title: pt84_107_3, scRNAseq

description: 10x Genomics

source_name: left femoral lymph node

value: left femoral lymph node


title: Gametocyte induction_Day 1, biol rep1

description:
Library name: R1-DAY1
fastq files from four lanes of the same flow cells were concatenated into one fastq file

value: complete medium


title: rat_HS-ICTO-2

description: Library name: Sample14


title: Gametocyte induction_Day 1, biol rep2

description:
Library name: R2-DAY1
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: pt79_107_1, scRNAseq

description: 10x Genomics


title: Untreated IκBα WT  rep1

description:
WT_CT1
RNAseq_INDs_ikBa_gene_quantification.txt (col. 15)

source_name: Untreated HT29 IκBα WT rep1


title: Gametocyte induction_Day -1, biol rep1

description:
Library name: R1-DAY-1
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: rat_HS-ICTO-1

description: Library name: Sample13


title: 6dpi, WVC4, scRNAseq

data_processing:
Single cell RNA-Seq FASTQ files were aligned to the human reference genome using CellRanger software (v 5.0.1) to generate raw count matrices for all the 4 different experimental conditions, named as MOCK, 1dpi, 3dpi and 6 dpi
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separeted values files and matrix files (Standard Cell Ranger Output)

growth_protocol: Tracheal basal cells isolated from a de-identified human lung specimen was expanded in PneumaCULT-Ex expansion media (StemCell Technologies, MA) and seeded on collagen-coated 24-well transwells. Once the cells reached confluence, media in the upper chamber of the transwell was removed and the media in the bottom chamber will be changed to PneumaCULT-ALI media (StemCell Technologies, MA) containing compounds including retinoic acid to induce cell differentiation. Differentiation efficiency on ALI day 21 was evaluated by measuring markers for ciliated cell (FOXJ1, ac-Tubulin), secretory cell (MUC5AC, CC10), and basal cells (TP63, KRT5) using immunofluorescence analysis.

extract_protocol:
Cells were removed at days 1, 3, and 6 days post-infection by adding 1 mL of accutase solution (Sigma A6964-100mL) into the basolateral side of the transwell. Cells were incubated at 37 degrees Celsius for 30 minutes until cells were detached.
Cells were centrifuged at 4 degrees celsius at 350 rpm for 5 minutes, were resuspended, and processed for scRNA-Seq on a 10× Genomics Chromium Controller using 5′ Next GEM v1.1 reagents (10× Genomics, Inc) according to the manufacturer’s protocol.

treatment_protocol: All ALI cultures were infected following BSL-3 guidelines. Specifically, ALI-differentiated cells at day 21 were inoculated on the apical surface by SARS- CoV-2 (“Seattle strain”, NR-52281) at a previously tested multiplicity of infection (MOI) of 0.1. After 2 hours, the virus-containing media in the apical chamber was removed and cells will be washed with PBS and continue to grow for 1, 3, and 6 days (days post infection, dpi). Mock infection condition will be performed in parallel using the same reagents without virus. Infection efficiency was determined by plaque assay (titer) performed on Vero-6 cells.


title: Doxy-treated IκBα SOFNF-kB  rep2

description:
M3_D2
RNAseq_INDs_ikBa_gene_quantification.txt (col. 14)

source_name: Doxy-treated HT29 IκBα mutant associating with p65 and p50 rep2

value: IκBalpha triple H84, E85, E86 to A mutant


title: Gametocyte induction_trophozoite control, biol rep1

description:
Library name: R1-Trophozoite_induction
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: 3dpi, WVC3, scRNAseq


title: rat_HS-3

description: Library name: Sample12

value: Implanted with HS scaffold


title: Doxy-treated IκBα SOFNF-kB  rep1

description:
M3_D1
RNAseq_INDs_ikBa_gene_quantification.txt (col. 13)

source_name: Doxy-treated HT29 IκBα mutant associating with p65 and p50 rep1


title: Asexual Schizont-stage tRNA, biol rep3

description:
Library name: S3-tRNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: rat_HS-2

description: Library name: Sample11


title: 1dpi, WVC2, scRNAseq


title: Asexual Trophozoite-stage tRNA, biol rep3

description:
Library name: T3-tRNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: rat_HS-1

description: Library name: Sample10