title: EV MEF, PlaB Z22, Biol Rep 2

city: Philadelphia

first: Yunyun

last: Zhou

state: Pennsylvania

address: 314 Chandler Street

institute: Fox Chase Cancer Center

description:
Library name: PB1_Z22_16
Transcriptomic

data_processing:
The sequencing reads were processed using the nf-core RNA-seq pipeline (version v3.11). Raw reads were first subjected to quality control with FastQC, low-quality reads and adapters were trimmed using Trim Galore. Cleaned reads were then aligned to the reference genome (GRCm38) using STAR aligner. Transcript-level quantification was performed using Salmon, providing normalized expression values for downstream analysis. Differential expression analysis was conducted using DESeq2 (version 1.45). Intron retention (IR) was analyzed using iREAD (version 0.8.9)
Assembly: GRCm38
Supplementary files format and content: raw_counts

source_name: EV MEF

growth_protocol: EV MEFs were grown on cell-culture treated plates with DMEM with 10% FBS.

extract_protocol:
RNA species from DMSO or PlaB-treated EV MEF cells were extracted using Magna RIP RNA-binding Protein Immunoprecipitation kit. RNA immunoprecipitation was performed with Z22 antibody following the manufacturer's instructions. Ribosomal RNA was removed using RiboMinus Core Module V2 and RiboMinus Concentration Module following the manufacturer’s instructions.
RNA fragmentation, cDNA reverse transcription, and Illumina sequencing library preparations were performed by the Novogene RIP-Seq services using the NEB Next Ultra II RNA Library Prep Kit for Illumina following the manufacturer’s instructions. Libraries were analyzed for fragment distributions using the 2100 Bioanalyzer RNA 6000 Nano Assay and quantified using the Qubit 2.0 Fluorometer. Followed by Illumina paired-end 150 (PE150) cycle sequencing on Illumina NovaSeq 6000.

treatment_protocol: EV MEFs were treated with DMSO or 50 nM Pladienolide B (PlaB) for 18 hours.

value: EV MEF

value: Mouse Embryonic Fibroblasts

value: PlaB


title: MM00263, follow-up, active

status: Public on Sep 14 2025

type: RNA

city: Oxford

first: Edmund

middle: C R

last: Watson

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

hyb_protocol: Xenium

scan_protocol: Xenium In Situ Analyzer

data_processing: Counts matrices and associated centroid and segmentation coordinates were read into Seurat for R. Following clustering and manual cell annotation, trephine data were tiled with 500 µm × 500 µm squares and clustered according to cell composition. CellChat analysis was performed to assess communication per tile.

label: Xenium 480 custom panel

molecule: total RNA

organism: Homo sapiens

source_name: multiple myeloma

label_protocol: Xenium samples were assessed with a 480-gene custom Xenium panel. Slides were processed on a 10x Xenium v1 platform (10X Genomics) including cell segmentation staining (10X Genomics, user guide CG000749, Rev A)

extract_protocol: Bone marrow trephine sections (5 µm-thick) were taken for Xenium.

treatment_protocol: Multiple myeloma patients were treated with Belantamab Mafodotin. Bone marrow trephines were collected before and after the treatment.

tag: tissue

value: Bone marrow trephine

tag: subject id

tag: subject status

value: relapse on-treatment


title: shYEATS4 rep3

type: SRA

city: Beijing

first: Zijun

last: Peng

address: Xueyuan road number 38

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
High-quality reads were aligned to the human reference genome (GRCh19) using HISAT2. The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM). Differentially expressed mRNAs and genes were selected using the DEseq2
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: MCF-7 cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was isolated using TRIzol reagent following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

tag: treatment

value: YEATS4 knockdown


title: EV MEF, PlaB Z22, Biol Rep 1

country: USA

description:
Library name: PB1_Z22_13
Transcriptomic

organism: Mus musculus

tag: cell type

tag: genotype


title: MM00075, follow-up, remission

value: remission on-treatment


title: shYEATS4 rep2


title: MM00075, screening

value: pre-treatment


title: WTKlf3MEFs Klf3 ChIP-seq Rep 2 INPUT

city: Sydney

first: Merlin

last: Crossley

state: NSW

address: UNSW

department: BABS

country: Australia

institute: University of New South Wales

library_source: genomic

data_processing:
ChiP-seq - After quality filtering and adaptor trimming using Trimmomatic v0.3.3 using the default parameters (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36) (Bolger et al. 2014), reads were aligned to the mm10/GRCm38 Mus musculus genome using Bowtie v2.2.9 (Langmead & Salzberg 2012) set to –very-sensitive. Aligned reads were filtered using samtools v1.3.1 (Danecek et al. 2021) to remove unmapped reads, non-primary alignments, and alignments with a mapping quality less than 10 (-F 1804 -q 10).
ChiP-seq - Peak calling for all datasets was done using the spp package (Kharchenko et al. 2008, Landt et al. 2012) after removing duplicates with Picard MarkDuplicates v1.109. A set of consistent peaks (IDR = 0.01 for KLF3-V5 or 0.05 for WDR5) were then identified using IDR2 (Landt et al. 2012, Li et al. 2011).
ChIP-seq - Read coverage tracks were generated using deepTools bamcoverage (Ramírez et al. 2016) with the filtered mapped reads, extending reads based on predicted fragment sizes from spp, and normalizing all samples to have the equivalent of 1 million mapped reads (-bs 1 --normalizeUsing CPM).
RNA-seq - Raw fastq files were quantified using Salmon v1.6.0 (Patro et al. 2017) in selective alignment mapping mode (--validateMappings --rangeFactorizationBins 4) using a GENCODE vM20 (Frankish et al. 2019) (based on Mus musculus mm10 genome). A decoy-aware index was built by concatenating the GRCm38 primary assembly genome to the end of the GENCODE vM20 transcriptome. The quantified .sf files are provided for each RNA-seq sample
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak, sf - plain-text, tab separated file with header generated after quantification by salmon

molecule: genomic DNA

source_name: Klf3-V5 ChIP-seq (INPUT) in Klf3-null MEF cells rescued by overexpressing  WT Klf3-V5

growth_protocol: Mouse embryonic fibroblast (MEF) cells were cultured in Dulbecco's modified Eagle's medium (DMEM) (Life Technologies, CA, USA) supplemented with 1% (v/v) Penicillin-Streptomycin-Glutamine (PSG) solution (Life Technologies, CA, USA) and 10% (v/v) fetal bovine serum (FBS) (Life Technologies, CA, USA). Cells were grown at 37°C in a 5% CO2 water-jacketed incubator.

extract_protocol:
ChIP experiments were performed as previously described (Schmidt et al. 2009). Approximately, 7x107-1x108 cells were used for each ChIP. Cells were crosslinked with 1% formaldehyde for 10 min and the reaction was quenched by 2.5 mM glycine. Fixed cells were washed with cold PBS and centrifuged at 2000 x g for 5 min. Fixed cells were sonicated at high voltage for 20 min (30 seconds on, 30 seconds off) using a Bioruptor (Diagenode) to obtain 200-300 bp DNA fragments. The fragmented chromatin was pulled down at 4°C overnight using an antibody against V5 (Life Technologies, #R960CUS) or WDR5 (Australian Biosearch, #13105S). Chromatin cross-linking was then reversed at 65°C overnight followed by DNA purification. Real-time qPCR was performed on ChIP DNA on an Applied Biosystems ViiA7 Real-time PCR system (Applied Biosystems) to confirm the success of the ChIP experiments before sending to next generation sequencing.
TruSeq DNA Sample Prep Kit

value: WT Klf3-V5

value: Klf3-null MEF cells

tag: chip antibody

value: input


title: WTKlf3MEFs Wdr5 ChIP-seq Rep 1

source_name: Wdr5 ChIP-seq in Klf3-null MEF cells rescued by overexpressing  WT Klf3-V5

value: WDR5 (Australian Biosearch, #13105S)


title: EV MEF, PlaB input, Biol Rep 2

description:
Library name: PB1_input_10
Transcriptomic


title: shYEATS4 rep1


title: WTKlf3MEFs Klf3 ChIP-seq Rep 1 INPUT


title: R254AKlf3MEFs Klf3 ChIP-seq Rep 1

source_name: Klf3-V5 ChIP-seq in Klf3-null MEF cells rescued by overexpressing R254A Klf3-V5

value: R254A Klf3-V5

value: V5 tag (Life Technologies, #R960CUS)


title: EV MEF, PlaB input, Biol Rep 1

description:
Library name: PB1_input_9
Transcriptomic


title: Apical buds of control plants exposed to 2 weeks of chilling, replicate 1 bulk RNAseq

city: Madrid

first: Daniela

last: Gomez Soto

address: Parque Científico y Tecnológico, UPM Campus de Montegancedo, Ctra, M-40, km 38

country: Spain

institute: CBGP

description:
Library name: Control rep. 1. Chilling2W bulk RNAseq
WT_1_CH2

data_processing:
Trimmed reads are mapped to reference genome with HISAT2
Assembly: P. tremula × alba INRA clone 717-1B4 genome (HAP2) and annotation files were used in these analyses.
Supplementary files format and content: For the bulk RNA-seq, processed data is the csv file containing the raw counts of each gene after mapping, in each sample.

organism: Populus tremula x Populus alba

source_name: Apical buds

growth_protocol: In vitro hybrid poplars (Populus tremula x alba INRA clone 717 1B4) were multiplied under sterile conditions in Murashige and Skoog (MS) medium (pH 5.7) supplemented with 2% sucrose, 0.5 mg/L each of indole acetic acid and indole butyric acid, and 0.7% (w/v) plant agar. After 4–5 weeks under long-day (16h light/8h dark) conditions with 65% relative humidity and 22°C, these plants were transferred to blond peat pots (pH 4.5). Plants were then grown for 4 weeks under the same long-day and 22°C conditions to achieve full apical growth before beginning phenological experiments.

extract_protocol:
To perform the bulk RNA extraction, two biological replicates were collected, in which each was made of 2 different plants. RNA extraction was performed by adding to grinded frozen buds tissue CTAB extraction buffer with 2% β-mercaptoethanol at 65ºC for 5-8 minutes, following by 3 washes with chloroform. After that, 7.5 M LiCl2:50mM EDTA was added, and samples were precipitated overnight at 4ºC. Next day, RNA was collected by centrifuging at 10.000 RPM for 20 minutes, the supernatant was discarded, and the pellet was resuspended using NR buffer (NZYTech, Lisboa, Portugal). RNA was then purified according to the manufacturer’s instructions of NZY RNA purification kit (NZYTech, Lisboa, Portugal). A total of 100 ng of extracted RNA was used to generate the RNA-seq libraries.
Libraries were generated from cDNA samples using the TruSeq Stranded mRNA Library Prep Kit (Nat Rev Genet. 2011 Sep 7;12(10):671-82) and they were sequenced on the Illumina platform (MACROGEN, Seúl, South Korea).

treatment_protocol: Four weeks after potting, the plants were exposed to eight weeks of short-day conditions to induce growth cessation and bud set. Plants of all genotypes were divided into two groups: The first group was harvested at this point (SD8W) at ZT7. The second group of plants was then exposed to two additional weeks of short-day conditions at 4°C, after which apical buds were collected, also at ZT7.

value: Apical buds

value: Wild type

value: 2 weeks of chilling


title: Apical buds of control plants exposed to 2 weeks of chilling, replicate 2 bulk RNAseq

description:
Library name: Control rep. 2. Chilling2W bulk RNAseq
WT_2_CH2


title: Apical buds of TEML2_2ox plants exposed to 2 weeks of chilling, replicate 2 bulk RNAseq

description:
Library name: TEML2_2 rep. 2 Chilling2W bulk RNAseq
TEML2_2_2_CH2


title: EV MEF, DMSO Z22, Biol Rep 2

description:
Library name: D1_Z22_8
Transcriptomic

value: EV MEF

value: DMSO


title: Apical buds of TEML2_2ox plants exposed to 2 weeks of chilling, replicate 1 bulk RNAseq

description:
Library name: TEML2_2 rep. 1. Chilling2W bulk RNAseq
TEML2_2_1_CH2


title: WTKlf3MEFs Klf3 ChIP-seq Rep 1

source_name: Klf3-V5 ChIP-seq in Klf3-null MEF cells rescued by overexpressing  WT Klf3-V5


title: EV MEF, DMSO Z22, Biol Rep 1

description:
Library name: D1_Z22_5
Transcriptomic

value: Mouse Embryonic Fibroblasts


title: shNC rep2

value: control


title: LAMA2 exon3-deficient hiPSC-derived myogenic precursor cells, differentiation run 4

city: Krakow

first: Krzysztof

last: Szade

address: Gronostajowa 7

country: Poland

institute: Jagiellonian University

description: Library name: IonCode_0336

data_processing:
Differential gene expression analysis was performed using the DESeq278 package from Bioconductor, with donor identity included as a covariate in the design formula to control for inter-individual variability. Genes with low expression (total counts ≤ 1 across all samples) were filtered out to reduce background noise. A DESeqDataSet object was constructed using the filtered count matrix and metadata, with the design formula ~ Exp + Group. To stabilize variance across the range of mean expression values variance stabilizing transformation (VST) was applied and VST-transformed data was used for exploratory analyses. Sample relationships were visualized using heatmaps based on Euclidean and Poisson distances, and principal component analysis (PCA) was conducted to assess clustering by experimental condition. Differential expression testing was carried out using the DESeq2 pipeline, and results were filtered based on adjusted p-values (FDR < 0.1) and log2 fold change thresholds. Shrinkage of log2 fold changes was performed using the apeglm method to improve interpretability. Annotated results were generated using the org.Hs.eg.db package to map gene symbols, Entrez IDs, and Ensembl IDs, and the top 100 genes were exported for further analysis. Gene set enrichment analysis (GSEA) was performed using the fgsea package, with genes ranked by log2 fold change and tested against hallmark gene sets from MSigDB.
Assembly: GRCh38
Supplementary files format and content: matrix.txt
Supplementary files format and content: Matrix with raw counts

source_name: hiPSC

growth_protocol: Myogenic precursors  were generated from control and LAMA2 exon3-deficient hiPSC using Skeletal Muscle Differentiation Kit (Amsbio)

extract_protocol:
Total RNA was isolated accordingly to Chomczynski and Sacchi method using Fenozol.
RNA libraries for a total of eight samples were prepared using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit

value: hiPSC

value: hiPSC-derived myogenic precursor cells

value: LAMA2 KO


title: Apical buds of TEML2_1ox plants exposed to 2 weeks of chilling, replicate 1 bulk RNAseq

description:
Library name: TEML2_1 rep. 1. Chilling2W bulk RNAseq
TEML2_1_1_CH2


title: EV MEF, DMSO input, Biol Rep 2

description:
Library name: D1_input_2
Transcriptomic


title: EV MEF, DMSO input, Biol Rep 1

description:
Library name: D1_input_1
Transcriptomic


title: LAMA2 exon3-deficient hiPSC-derived myogenic precursor cells, differentiation run 3

description: Library name: IonCode_0335


title: CCA tumor scRNAseq ZhuLZ_dCCA_C

city: JiNan

first: Anda

last: Shi

address: Culture West Road num 107

institute: Qilu Hospital

description:
CCA tumor,scRNAseq
10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software（version2.20）. Sample demultiplexing, barcode processing and single-cell 3’gene counting by using the Cell Ranger pipeline(https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger，version 6.1.1) and scRNA-seq data were aligned to Ensembl genome GRCh38/GRCm38 reference genome.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bile duct

extract_protocol: Human bile duct tissue was obtained from patients . Place a sterile RNase-free culture dish containing an appropriate amount of calcium free and magnesium-free 1 × PBS on ice, the tissue was transferred into the culture dish and cut it into 0.5 mm2 pieces, the tissues were washed with 1 × PBS, and remove as many non-purpose tissues as possible such as blood stains and fatty layers.Tissues were dissociated into single cells in dissociation solution (0.35% collagenase IV5,2 mg/ml papain, 120 Units/ml DNase I) in 37 ℃water bath with shaking for 20 min at 100 rpm. Digestion was terminated with 1× PBS containing 10% fetal bovine serum（FBS,V/V）, then pipetting 5-10 times with a Pasteur pipette.The resulting cell suspension was filtered by passing through 70-30um stacked cell strainer and centrifuged at 300g for 5 min at 4 °C. The cell pellet was resuspended in 100ul 1× PBS (0.04% BSA) and added with 1 ml 1× red blood cell lysis buffer（MACS 130-094-183, 10×）and incubated at room temperature or on ice for 2-10 min to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 300g for 5 min at room temperature. The suspension was resuspended in 100 μl Dead Cell Removal MicroBeads(MACS 130-090-101) and remove dead cells using Miltenyi ® Dead Cell Removal Kit (MACS 130-090-101). Then the suspension was resuspended in 1× PBS(0.04% BSA) and centrifuged at 300 g for 3 min at 4 °C（repeat twice）. The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion , which needed to be above 85%, single cell suspensions were counted using a haemocytometer/ Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.

value: bile duct

tag: tumor type

value: dCCA

tag: Sex

value: Male

tag: age

value: 67 years old


title: LAMA2 exon3-deficient hiPSC-derived myogenic precursor cells, differentiation run 2

description: Library name: IonCode_0334


title: CCA tumor scRNAseq ZhangLZ_dCCA_C

description:
CCA tumor,scRNAseq
10x Genomics

value: 66 years old


title: Apical buds of TEML1_2ox plants exposed to 2 weeks of chilling, replicate 2 bulk RNAseq

description:
Library name: TEML1_2 rep. 2 Chilling2W bulk RNAseq
TEML1_2_2_CH2


title: LAMA2 exon3-deficient hiPSC-derived myogenic precursor cells, differentiation run 1

description: Library name: IonCode_0333


title: Mouse,PyMT,Lung,Chronic Stress,rep2

city: Shanghai

first: Pengfei

last: Liu

address: 150 Jimo Road

institute: Shanghai East Hospital, Tongji University School of Medicine

description: Library name: PyMT_Lung_CS_rep2

data_processing:
Raw reads were quality-controlled, demultiplexed and aligned to the mm10 mouse reference genome and PyMT using Cellranger (version 5.0.0, 10X Genomics). The PyMT gene sequence was retrieved from GeneBank database (accession number AAB59900.1). Cells with less than 250 genes, or greater than 4,000 genes, or over 10% reads aligning to mitochondrial genes, or gene number greater than 0.8 per UMI were filtered. DoubletFinder was employed to identify and remove doublets. SCTransform function in Seurat was applied to identify genes with high variance for normalization, in which mitochondrial mapping percentage was used as a parameter for covariant correction. IntegrateData function in Seurat, jointly integrating Canonical correlation analysis (CCA) and Mutual nearest neighbors (MNN) algorithms, was performed to remove batch effect between samples and then merge together.
1. Raw data processing:    - Base calling: Illumina bcl2fastq v2.20 (--mask-short-adapter-reads=8)    - Demultiplexing: Cell Ranger mkfastq v5.0.0 (10x Genomics)
2. Reference genome alignment:    - Alignment software: Cell Ranger count v5.0.0    - Reference genome: mm10 (GRCm38) + PyMT transgene (GenBank: AAB59900.1)    - Parameters: --include-introns=false --chemistry=auto
3. Quality control:    - Cell filtering criteria:      * Minimum genes/cell: 250      * Maximum genes/cell: 4,000      * Mitochondrial gene cutoff: <10%      * UMI ratio filter: genes/UMI < 0.8    - Doublet removal: DoubletFinder v2.0.3 (expected_doublet_rate=0.05)
4. Normalization & batch correction:    - Normalization method: SCTransform (Seurat v4.3.0)      * Variance stabilization: 3,000 most variable genes      * Covariates: percent.mt (mitochondrial content)    - Integration:      * Method: CCA + MNN (IntegrateData in Seurat)      * Anchors used: 2,000      * Dimensionality: 30 PCs
Assembly: genome build: GRCm38/mm10 ；PyMT transgene (GenBank: AAB59900.1)
Supplementary files format and content: Filtered_Feature_Barcode_Matrix .h5 HDF5; A sparse matrix containing: - Gene expression counts (UMIs) for cells passing QC filters - Rows: Features (genes + PyMT transgene) - Columns: Cell barcodes

molecule: polyA RNA

source_name: lung

growth_protocol: Animal housing: 12-hour light/dark cycle, 22±1°C, 50-60% humidity, ad libitum access to standard chow and water. Tumor monitoring: Palpation twice weekly from 6 weeks of age

extract_protocol:
The lung tissues were minced, and then digested at 37 °C for 30 min using an enzyme cocktail including 150 U/mL of Collagenase Ⅳ, 20 U/mL of Dispase, 5 U/mL of Elastase and 0.33 U/mL of DNase I. The cell solution was filtered through a 40 μm strainer to obtain single-cell suspension. Acridine orange (AO) and propidium iodide (PI) were used to stain living cells. WOLF® Cell Sorter (NanoCellect) was used for cell sorting.
Sorted single cells were diluted in DMEM/F12 with 10% FBS, and loaded on a Chromium Controller to generate single-cell gel bead emulsions, targeting 20,000-30,000 cells for each tumor tissue (n=2 in the current study). Single-cell 3′ RNA-seq libraries were generated according to the manufacturer’s instructions (Chromium Single Cell 3′ Reagent v2 Chemistry Kit, 10X Genomics, Inc.), followed by a sequencing analysis to reach an average depth of ~ 200,000 reads per cell using Illumina Novaseq 6000 system.

treatment_protocol: Female mice in the CS group received one kind of unpredictable stress stimulation at a random time point between 7 am and 7 pm every day during the chronic stress period. The stress types included noise stimulation (80 decibels for 120 min each time), restraint stimulation (120 min each time), elevated platform stimulation (10 cm diameter, 1.2 m height of a platform for 60 min each time), shaking stimulation (60 rpm for 60 min each time), and somatosensory stimulation (tail-clamping for 1 min, repeating 3 times within 10 min each time). Each mouse was unpredictably given one of the six stimuli by a random selection every day.

value: lung

value: mixed cell population

value: MMTV-PyMT transgenic

value: subjected to four weeks of chronic mild unpredictable stress

tag: batch


title: control hiPSC-derived myogenic precursor cells, differentiation run 4

description: Library name: IonCode_0340


title: para-tumor scRNAseq YP_dCCA_N

description:
para-tumor,scRNAseq
10x Genomics

value: 63 years old


title: Mouse,PyMT,Lung,Chronic Stress,rep1

description: Library name: PyMT_Lung_CS_rep1


title: Apical buds of TEML1_2ox plants exposed to 2 weeks of chilling, replicate 1 bulk RNAseq

description:
Library name: TEML1_2 rep. 1. Chilling2W bulk RNAseq
TEML1_2_1_CH2

value: Apical buds

value: 2 weeks of chilling


title: shNC rep3


title: Apical buds of TEML1_1ox plants exposed to 2 weeks of chilling, replicate 2 bulk RNAseq

description:
Library name: TEML1_1 rep. 2 Chilling2W bulk RNAseq
TEML1_1_2_CH2


title: WTKlf3MEFs Klf3 ChIP-seq Rep 2

value: WT Klf3-V5

value: Klf3-null MEF cells

value: V5 tag (Life Technologies, #R960CUS)


title: CCA tumor scRNAseq YP_dCCA_C

description:
CCA tumor,scRNAseq
10x Genomics


title: Mouse,PyMT,Lung,Native Control,rep2

description: Library name: PyMT_Lung_NC_rep2

value: untreated


title: control hiPSC-derived myogenic precursor cells, differentiation run 3

description: Library name: IonCode_0339

value: hiPSC

value: hiPSC-derived myogenic precursor cells

value: control


title: Apical buds of TEML2_1ox plants exposed to 2 weeks of chilling, replicate 2 bulk RNAseq

description:
Library name: TEML2_1 rep. 2 Chilling2W bulk RNAseq
TEML2_1_2_CH2


title: Mouse,PyMT,Lung,Native Control,rep1

description: Library name: PyMT_Lung_NC_rep1


title: shNC rep1


title: Apical buds of TEML1_1ox plants exposed to 2 weeks of chilling, replicate 1 bulk RNAseq

description:
Library name: TEML1_1 rep. 1. Chilling2W bulk RNAseq
TEML1_1_1_CH2


title: Apical buds of control plants exposed to 8 weeks of short-day conditions, replicate 2 bulk RNAseq

description:
Library name: Control rep. 2. SD8W bulk RNAseq
WT_2_SD8

value: Wild type

value: 8 weeks of short-day


title: control hiPSC-derived myogenic precursor cells, differentiation run 2

description: Library name: IonCode_0338


title: CCA tumor scRNAseq WZG_dCCA_C

description:
CCA tumor,scRNAseq
10x Genomics

value: bile duct

value: dCCA

value: Male

value: 82 years old


title: TGF-beta-K-80003-2

city: Xiamen

first: Lijun

last: Cai

address: No. 668, Jinhu Road

department: Central Laboratory,

institute: Zhongshan Hospital (Xiamen), Fudan University

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Expression analysis In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
GO and KEGG enrichment analysis GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less than 0.05. And topGO was used to plot DAG. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG). We used scripts in house to enrich significant differential expression gene in KEGG pathways.
Novel transcripts prediction After assembling a transcriptome from one or more samples, Cuffcompare, a tool of Cufflinks v2.2.1, compared assembly to known transcripts. Then, novel transcripts can be predicted via results of Cuffcompare.
Alternative splicing analysis rMATs v4.1.0 is a computational tool to detect differential alternative splicing events from RNA-Seq data. And resulting bam files of aligner HISAT2 had been used as input during the analysis. SNV analysis Samtools v0.1.19 with command mpileup and Bcftools v0.1.19 were used to do SNV calling. Differential exon usage By differential exon usage (DEU), we mean changes in the relative usage of exons caused by the experimental condition. The relative usage of an exon is defined as number of transcripts from the gene that contain this exonnumber of all transcripts from the gene The basic concept can be summarized as follows. For each exon (or part of an exon) and each sample, we count how many reads map to this exon and how many reads map to any of the other exons of the same gene. We consider the ratio of these two counts, and how it changes across conditions, to infer changes in the relative exon usage. In the case of an inner exon, a change in relative exon usage is typically due to a change in the rate with which this exon is spliced into transcripts (alternative splicing). Note, however, that DEU is a more general concept than alternative splicing, since it also includes changes in the usage of alternative transcript start sites and polyadenylation sites, which can cause differential usage of exons at the 5’ and 3’ boundary of transcripts. To analysis DEU, we used Bioconductor package DEXSeq (V 1.21.1).
Principal component analysis This is another way to visualize sample-to-sample distances. In this ordination method, the data points (here, the samples) are projected onto the 2D plane such that they spread out in the two directions that explain most of the differences. The x-axis is the direction that separates the data points the most. The values of the samples in this direction are written PC1. The y-axis is a direction (it must be orthogonal to the first direction) that separates the data the second most. The values of the samples in this direction are written PC2. The percent of the total variance that is contained in the direction is printed in the axis label. Note that these percentages do not add to 100%, because there are more dimensions that contain the remaining variance (although each of these remaining dimensions will explain less than the two that we see). This analysis has been dealt with R language with FPKM value as the input.
Assembly: GRCm39.107
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Liver

extract_protocol:
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers.
First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: Liver

value: mHSC

value: Primary mouse hepatic stellate cells

value: WT


title: control hiPSC-derived myogenic precursor cells, differentiation run 1

description: Library name: IonCode_0337


title: CCA tumor scRNAseq SLB_pCCA_C

description:
CCA tumor,scRNAseq
10x Genomics

value: pCCA

value: 71 years old


title: Apical buds of control plants exposed to 8 weeks of short-day conditions, replicate 1 bulk RNAseq

description:
Library name: Control rep. 1. SD8W bulk RNAseq
WT_1_SD8

value: Apical buds


title: Apical buds of TEML2_2ox plants exposed to 8 weeks of short-day conditions, replicate 1 bulk RNAseq

description:
Library name: TEML2_2 rep. 1. SD8W bulk RNAseq
TEML2_2_1_SD8


title: KI213S1

city: Leiden

first: Sebastiaan

middle: Johannes

last: van Kampen

address: Sylviusweg 62

country: Netherlands

institute: LUMC

data_processing:
STAR_2.4.2a mapping to reference genome
read count analysis HTSeq 0.6.1
Assembly: hg19
Supplementary files format and content: raw read counts in matrix table

growth_protocol: hiPSCs were maintained in Essential 8 medium and grown till 80-90% confluency (Day 0). Next, medium was aspirated and the cells were washed once with dPBS (GIBCO, 14190094). Subsequently, cells were fed with RPMI-1640-Medium-GlutaMAX™Supplement-HEPES (GIBCO, 72400-021) supplemented with 0.5 mg/mL human recombinant (Sigma-Aldrich, A9731), 0.2 mg/mL L-Ascorbic Acid 2-Phosphate (Sigma-Aldrich, A8960), and 4 µM CHIR99021 (Sigma-Aldrich, 361559). After 2 days (Day 2), medium was aspirated and cells were washed once with RPMI-1640-Medium-GlutaMAX™Supplement-HEPES, followed by addition of RPMI-1640-Medium-GlutaMAX™Supplement-HEPES supplemented with 0.5 mg/mL human recombinant (Sigma-Aldrich, A9731), 0.2 mg/mL L-Ascorbic Acid 2-Phosphate , and 5 µM IWP2 (Sigma-Aldrich, 681671). On day 4 and day 6, cells were refreshed with RPMI-1640-Medium-GlutaMAX™Supplement-HEPES supplemented with 0.5 mg/mL human recombinant and 0.2 mg/mL L-Ascorbic Acid 2-Phosphate. From day 8 onwards, cells were maintained in RPMI-1640-Medium-GlutaMAX™-Supplement-HEPES supplemented with B-27™Supplement (50x)-serum free (GIBCO, 17504001). Spontaneous beating cardiomyocytes could be observed between day 8 and day 10. hiPSC-derived cardiomyocytes were subsequently dissociated for downstream applications with TrypLE™ Select Enzyme (10x)-no phenol red (GIBCO, A1217703) for a maximum of 20 minutes at 37oC. Cardiomyocytes were seeded at a density of 100,000 cells/cm2 in Geltrex-coated wells.

extract_protocol:
Qiagen RNeasy mini kit (74104)
Truseq RNA stranded polyA

treatment_protocol: Baseline conditions

value: hiPSC-derived cardiomyocytes

value: DSP p.Arg1113X/WT

value: 30 days post-differentiation


title: TGF-beta-1

value: TGF-β


title: para-tumor scRNAseq LFY_pCCA_HGIEN

description:
para-tumor,scRNAseq
10x Genomics

value: Female

value: 56 years old


title: Control-2

value: Control


title: Isolated transmural sections from a single explanted ACM heart

data_processing:
Reads 2 were mapped to the reference transcriptome (created from the genomes downloaded from the UCSC genome browser; ERCC Spike-in sequences and mitochondrial sequences were added) in sense direction using BWA MEM (version 0.7.10) with default parameters. In the reference transcriptome , all exons of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 were used for demultiplexing, reads 1 contain the cel-specific barcodes and the UMI-sequence and a polyT-stretch (see: CEL-seq.2.demultiplexing.barcodes.pdf). After mapping, a UMI-correction was applied to the read and barcode counts files to generate unique transcript count tables as described before (Grun 2014,PMID: 24747814 and Muraro 2016,PMID: 27693023). For details, see the online methods and supplementary of the manuscript.
Assembly: hg19
Supplementary files format and content: Read-, UMI(Barcode)-, Transcript-, count tables for mapped reads per cell as tab separated values (.tsv) for all sections. The first column lists official gene symbols followed by the chromosome name, separated by a double underscore. Every other column contains the read/UMI/transcript counts per sections.
Library strategy: Spatial Transcriptomics

source_name: Heart

growth_protocol: Primary cardiac tissue

extract_protocol:
mRNA extraction, barcoding, reverse transcription and in vitro transcription were performed as described (Junker et al., 2014, PMID: 25417113) using the Message Amp II kit (Ambion). See online methods and supplementary of the manuscript. After isolation, we cryosectioned samples, extracted RNA from the individual sections, and amplified and barcoded mRNA using the CEL-seq protocol as in (Junker 2014, PMID: 25417113), but with CEL-Seq v2 reverse transcription primers; See online methods and supplementary of the manuscript. Illumina TRU-seq libraries were constructed CEL-Seq v1 (but with CEL-Seq sample barcodes), as in (Junker et al 2014); See online methods and supplementary of the manuscript.
Truseq RNA stranded polyA

treatment_protocol: A transmural cross-section of the heart was positioned perpendicular to the sectioning axis, frozen and cryo-sectioned as described (Junker et al., 2014) with a sectioning width of 20 mm. See online methods and supplementary of the manuscript

value: Heart

tag: diagnosis

value: ACM

tag: disease state

value: End stage

value: DSP p.Lys569X/WT

value: Adult


title: TGF-beta-K-80003-1

value: Liver

value: mHSC

value: Primary mouse hepatic stellate cells


title: KI212S1


title: CCA tumor scRNAseq LFY_pCCA_C

description:
CCA tumor,scRNAseq
10x Genomics

value: bile duct

value: pCCA


title: KI211S1

value: hiPSC-derived cardiomyocytes


title: Apical buds of TEML2_1ox plants exposed to 8 weeks of short-day conditions, replicate 2 bulk RNAseq

description:
Library name: TEML2_1 rep. 2. SD8W bulk RNAseq
TEML2_1_2_SD8

value: Apical buds

value: 8 weeks of short-day


title: Acropora millepora 2 clicktags

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

institute: Centre for Genomic Regulation

description:
Library name: Sample 4
Clicktag barcodes reads necessary to demultiplex conditions. See Readme_ClickTag_demultiplexing.xlsx file for detailed description and barcodes used.

data_processing:
scRNA-seq: We used CellRanger 6.1.1 (10X Genomics) to map reads and count unique molecular identifiers (UMIs) per gene per cell. We used the --force-cells flat to set a constant number of 20,000 per experiment (well in excess of the expected number cells for each case, as we intended to remove non-cells from the dataset using our own procedure; see below). We used whole gene bodies to guide the mapping of reads to the genome (--transcriptome flag). For details on clicktag barcode demultiplexing see Readme_ClickTag_demultiplexing.xlsx file.
Assembly: Acropora millepora: GCF_013753865.1, Stylophora pistillata: GCF_002571385.2
Supplementary files format and content: TSV file with the gene IDs (in the same order as in the UMI matrix, mtx file)
Supplementary files format and content: TSV file with CellIDs and associated metadata (in the same order as in the UMI matrix, mtx file)
Supplementary files format and content: MTX file containin gene x cell UMI counts

organism: Acropora millepora

source_name: Whole adult specimens

extract_protocol:
Whole-adult specimens were fixed and dissociated before sorting single-cells for scRNAseq.
Cells were fixed using the ACME protocol (10.1186/s13059-021-02302-5), FACS sorted, and processed with the 10X Genomics Chromium Single Cell 3' scRNAseq v3.1 kit.

value: Whole adult specimens


title: Apical buds of TEML2_1ox plants exposed to 8 weeks of short-day conditions, replicate 1 bulk RNAseq

description:
Library name: TEML2_1 rep. 1. SD8W bulk RNAseq
TEML2_1_1_SD8


title: Apical buds of TEML1_2ox plants exposed to 8 weeks of short-day conditions, replicate 2 bulk RNAseq

description:
Library name: TEML1_2 rep. 2. SD8W bulk RNAseq
TEML1_2_2_SD8


title: para-tumor scRNAseq WZG_dCCA_N

description:
para-tumor,scRNAseq
10x Genomics

value: dCCA

value: Male

value: 82 years old


title: WT ATCC4S1

value: DSP WT/WT

value: 30 days post-differentiation


title: KPC-3403 Whole Tumor

city: Baltimore

first: Heng Chung

last: Kung

state: Maryland

address: 1650 Orleans Street

department: Department of Oncology

institute: Johns Hopkins University School of Medicine

data_processing:
The demultiplexing, barcode processing, gene counting were conducted using CellRanger v6.1.1 (10X Genomics)
Assembly: mm10
Supplementary files format and content: Tab separated values and matrix files

source_name: KPC PDAC Orthotopic Tumor

extract_protocol:
Murine orthotopic pancreatic tumors were dissected and collected on day 13 after tumor implantation for scRNA-seq processing. Tumors were mechanically and enzymatically processed with the mouse Miltenyi Tumor Dissociation Kit (Miltenyi Biotec) and gentleMACS Octo Dissociator (Miltenyi Biotec). Samples were then filtered through 100 µm strainer, which was then washed with 10 mL T cell media. Cell suspensions were centrifuged at 1500 RPM for 5 minutes. Cell pellets were resuspended in 10 mL T cell media, filtered through 100 µm strainer, and centrifuged again at 1500 RPM for 5 minutes.  For fibroblast enrichment, cells were resuspended with PBS and blocked with anti-mouse Fc antibody (BD Biosciences) in FACS buffer for 10 minutes on ice. Cells were then stained with CD45-AF657 (BioLegend clone 30-F11, 1:20), CD31-AF647 (BioLegend clone 390, 1:20), EPCAM-AF647 (BioLegend, clone G8.8, 1:20), and TER119-AF647 (BioLegend clone TER-119 1:20) for 30 minutes on ice. Single cell suspension was mixed every 10 minutes. Cells were washed with PBS twice, resuspended at 5-10 million cells/mL in T cell media, and filtered through 35 µm flow cytometry tubes (Falcon 352235). Sorting for CD45-, CD31-, EPCAM-, and TER119-negative cells was performed to obtain the fibroblast enriched fraction. Both the unenriched and enriched samples were washed and resuspended to cell concentration of 700-1200 cells/µL in PBS + 0.1% BSA for loading onto 10X Chromium microfluidic chips.
Single-cell capture, barcoding, and library preparation was performed using 10X Chromium Single Cell 5’ R2 chemistry according to the manufacturer’s protocol (#CG000207).

value: KPC PDAC Orthotopic Tumor

value: Whole tumor single cells suspension

tag: strain


title: WT ATCC3S1


title: Acropora millepora 2

description: Library name: Sample 2


title: Apical buds of TEML2_2ox plants exposed to 8 weeks of short-day conditions, replicate 2 bulk RNAseq

description:
Library name: TEML2_2 rep. 2. SD8W bulk RNAseq
TEML2_2_2_SD8


title: para-tumor scRNAseq SKF_pCCA_N

description:
para-tumor,scRNAseq
10x Genomics

value: Female

value: 60 years old


title: CCA tumor scRNAseq SKF_pCCA_C

description:
CCA tumor,scRNAseq
10x Genomics


title: TGF-beta-2

value: Liver

value: mHSC

value: WT

value: TGF-β


title: KI214S1

value: hiPSC-derived cardiomyocytes

value: DSP p.Arg1113X/WT


title: Apical buds of TEML1_1ox plants exposed to 8 weeks of short-day conditions, replicate 2 bulk RNAseq

description:
Library name: TEML1_1 rep. 2. SD8W bulk RNAseq
TEML1_1_2_SD8

value: Apical buds

value: 8 weeks of short-day


title: Acropora millepora 1

description: Library name: Sample 1

value: Whole adult specimens


title: Control-1

value: Primary mouse hepatic stellate cells

value: Control


title: WT ATCC1S1

value: DSP WT/WT


title: KPC-4545 Whole Tumor


title: Apical buds of TEML1_1ox plants exposed to 8 weeks of short-day conditions, replicate 1 bulk RNAseq

description:
Library name: TEML1_1 rep. 1. SD8W bulk RNAseq
TEML1_1_1_SD8


title: KPC-4545 Enriched Cancer Associated Fibroblast

value: Enriched cancer associated fibroblast


title: Acropora millepora 1 clicktags

description:
Library name: Sample 3
Clicktag barcodes reads necessary to demultiplex conditions. See Readme_ClickTag_demultiplexing.xlsx file for detailed description and barcodes used.


title: PC12-DG-B-1

status: Public on Sep 13 2025

city: 北京市

first: Renjun

last: Yang

state: 北京

address: 双清路18号林业大学北门

institute: RCEES

description:
PC12_core_table_gene.xls
PC12_DG_B

data_processing:
Remove the reads containing the connector
Remove reads with unknown base N content greater than 5%
Remove low-quality reads (we define reads with a mass value of less than 15 Accounting for more than 20% of the total base number of the reads as low-quality reads).The filtered "clean reads" is saved in fastq format
Software information: soapnuke， version： v1.5.2
Assembly: GCF_000001405.39_GRCh38.p13 and GCF_000001895.5_Rnor_6.0
Supplementary files format and content: xls，gene expression level

organism: Rattus norvegicus

source_name: Adrenal gland

growth_protocol: Cells are cultred with DMEM/F-12 medium supplemented with 1% N2, 2% B27, 20 ng/mL FGF2, and 1% Penicillin/Streptomycin

extract_protocol:
RNA was extracted with RNA extraction kit.
Total RNA was processed by mRNA enrichment method. mRNA enrichment: the mRNA with PolyA tail was enriched by magnetic beads with OligoDT. The obtained RNA was fragmented with the interruption buffer, and the random N6 primers were reverse transcribed, and then the two strands of cDNA were synthesized to form double stranded DNA. The ends of the synthesized double stranded DNA were flattened and phosphorylated at the 5 'end, the 3' end formed a protruding "a" sticky end, and then connected to a bubbly joint with protruding "t" at the 3 'end. The ligation products were amplified by PCR with specific primers. The PCR product was thermally denatured into a single strand, and then the single strand DNA was cyclized with a segment bridge primers to obtain a single strand circular DNA library. The constructed library was qualified for quality inspection and sequenced (BGI MGI2000).

treatment_protocol: Cells are treated with 1 μM IMZ, CYC, TDCIPP or 0.1% DMSO for 8 days.

value: Adrenal gland

value: rat pheochromocytoma cell

value: DG 100 nM


title: Apical buds of TEML1_2ox plants exposed to 8 weeks of short-day conditions, replicate 1 bulk RNAseq

description:
Library name: TEML1_2 rep. 1. SD8W bulk RNAseq
TEML1_2_1_SD8


title: PC12-AO2246-B-1

address: 双清路18号林业大学北门

description:
PC12_core_table_gene.xls
PC12_AO2246_B


title: PC12-CYC-B-1

address: 双清路18号林业大学北门

description:
PC12_core_table_gene.xls
PC12_CYC_B

value: CYC 1 μM


title: WT ATCC2S1

value: 30 days post-differentiation


title: PC12-CTRL-B-1

address: 双清路18号林业大学北门

description:
PC12_core_table_gene.xls
PC12_CTRL_B

value: 0.1% DMSO


title: KPC-3403 Enriched Cancer Associated Fibroblast

value: KPC PDAC Orthotopic Tumor


title: PC12-TnBP-B-1

address: 双清路18号林业大学北门

description:
PC12_core_table_gene.xls
PC12_TnBP_B

value: WT

value: TnBP 1 μM


title: PC12-BHT-Q-A-1

address: 双清路18号林业大学北门

description:
PC12_core_table_gene.xls
PC12_BHT_Q_A

value: BHT-Q 100 nM


title: PC12-BHT-Q-B-1

address: 双清路18号林业大学北门

description:
PC12_core_table_gene.xls
PC12_BHT_Q_B


title: PC12-TDCIPP-B-1

address: 双清路18号林业大学北门

description:
PC12_core_table_gene.xls
PC12_TDCIPP_B

value: TDCIPP 1 μM


title: PC12-BHT-B-1

address: 双清路18号林业大学北门

description:
PC12_core_table_gene.xls
PC12_BHT_B

value: BHT 100 nM


title: PC12-AO2246-A-1

address: 双清路18号林业大学北门

description:
PC12_core_table_gene.xls
PC12_AO2246_A


title: PC12-DG-A-1

address: 双清路18号林业大学北门

description:
PC12_core_table_gene.xls
PC12_DG_A


title: PC12-IMZ-B-1

address: 双清路18号林业大学北门

description:
PC12_core_table_gene.xls
PC12_IMZ_B

value: IMZ 1 μM


title: PC12-CYC-A-1

address: 双清路18号林业大学北门

description:
PC12_core_table_gene.xls
PC12_CYC_A


title: PC12-TnBP-A-1

address: 双清路18号林业大学北门

description:
PC12_core_table_gene.xls
PC12_TnBP_A


title: PC12-IMZ-A-1

address: 双清路18号林业大学北门

description:
PC12_core_table_gene.xls
PC12_IMZ_A


title: SK-AO2246-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
SK_AO2246_B

source_name: Brain

value: Brain

value: SK-N-SH

value: human neuroblastoma


title: PC12-CTRL-A-1

address: 双清路18号林业大学北门

description:
PC12_core_table_gene.xls
PC12_CTRL_A


title: PC12-BHT-A-1

address: 双清路18号林业大学北门

description:
PC12_core_table_gene.xls
PC12_BHT_A


title: SK-BHT-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
SK_BHT_B


title: SK-BHT-Q-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
SK_BHT_Q_B


title: SK-TnBP-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
SK_TnBP_B


title: SK-CTRL-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
SK_CTRL_B


title: SK-TDCIPP-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
SK_TDCIPP_B


title: NSC-AO2246-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_AO2246_B

source_name: Blastocyst

value: Blastocyst

value: neural stem cells


title: NSC-AO168-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_AO168_B


title: NSC-TBHQ-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_TBHQ_B

value: TBHQ 100 nM


title: NSC-BHT-COOH-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_BHT_COOH_B

value: BHT-COOH 100 nM


title: NSC-BHT-Q-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_BHT_Q_B


title: NSC-BHT-ql-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_BHT_ql_B

value: BHT-quinol 100 nM


title: PC12-TDCIPP-A-1

address: 双清路18号林业大学北门

description:
PC12_core_table_gene.xls
PC12_TDCIPP_A

value: Adrenal gland

value: rat pheochromocytoma cell


title: NSC-TDCIPP-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_TDCIPP_B


title: NSC-BHT-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_BHT_B


title: NSC-BHA-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_BHA_B

value: BHA 100 nM


title: NSC-DTBP-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_DTBP_B

value: WT

value: DTBP 100 nM


title: NSC-BHT-CHO-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_BHT_CHO_B

value: BHT-CHO 100 nM


title: NSC-TPHP-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_TPHP_B

value: TPHP 1 μM


title: NSC-TnBP-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_TnBP_B

value: TnBP 1 μM


title: NSC-TCEP-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_TCEP_B

value: TCEP 1 μM


title: NSC-TEP-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_TEP_B

value: TEP 1 μM


title: NSC-CYC-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_CYC_B

value: CYC 1 μM


title: NSC-IMI-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_IMI_B

value: IMI 1 μM


title: NSC-CTRL-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_CTRL_B

value: Blastocyst

value: 0.1% DMSO


title: SK-DG-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
SK_DG_B

value: Brain

value: SK-N-SH

value: human neuroblastoma

value: DG 100 nM


title: NSC-IMZ-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_IMZ_B

value: neural stem cells

value: IMZ 1 μM


title: NSC-ACE-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_ACE_B

value: WT

value: ACE 1 μM


title: SK-CYC-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
SK_CYC_B


title: NSC-DG-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_DG_B


title: SK-BHT-Q-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
SK_BHT_Q_A

value: BHT-Q 100 nM


title: SK-BHT-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
SK_BHT_A

value: BHT 100 nM


title: SK-AO2246-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
SK_AO2246_A


title: SK-TDCIPP-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
SK_TDCIPP_A

value: TDCIPP 1 μM


title: SK-DG-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
SK_DG_A


title: SK-TnBP-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
SK_TnBP_A

value: TnBP 1 μM


title: SK-CTRL-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
SK_CTRL_A


title: NSC-AO2246-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_AO2246_A


title: NSC-DG-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_DG_A


title: NSC-TBHQ-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_TBHQ_A

value: TBHQ 100 nM


title: NSC-BHA-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_BHA_A

value: BHA 100 nM


title: NSC-DTBP-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_DTBP_A

value: DTBP 100 nM


title: NSC-BHT-CHO-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_BHT_CHO_A

value: Blastocyst

value: BHT-CHO 100 nM


title: NSC-AO168-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_AO168_A


title: NSC-BHT-COOH-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_BHT_COOH_A

value: BHT-COOH 100 nM


title: NSC-BHT-ql-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_BHT_ql_A

value: BHT-quinol 100 nM


title: NSC-TDCIPP-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_TDCIPP_A


title: NSC-BHT-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_BHT_A


title: NSC-BHT-Q-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_BHT_Q_A


title: NSC-TPHP-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_TPHP_A

value: TPHP 1 μM


title: NSC-TEP-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_TEP_A

value: TEP 1 μM


title: NSC-TnBP-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_TnBP_A

value: neural stem cells


title: NSC-IMZ-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_IMZ_A

value: IMZ 1 μM


title: NSC-CYC-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_CYC_A

value: WT

value: CYC 1 μM


title: NSC-TCEP-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_TCEP_A

value: TCEP 1 μM


title: NSC-IMI-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_IMI_A

value: IMI 1 μM


title: SK-CYC-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
SK_CYC_A

value: Brain

value: SK-N-SH

value: human neuroblastoma


title: NSC-ACE-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_ACE_A

value: ACE 1 μM


title: TPHP-2-1

address: 双清路18号林业大学北门

data_processing:
Remove the reads containing the connector
Remove reads with unknown base N content greater than 5%
Remove low-quality reads (we define reads with a mass value of less than 15 Accounting for more than 20% of the total base number of the reads as low-quality reads).The filtered "clean reads" is saved in fastq format
Software information: soapnuke， version： v1.5.2
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: xls，gene expression level

source_name: ES-derived monolayer cells

growth_protocol: Monolayer differentiation was cultured on 24-well plates in E6 medium and the differentiation lasted for 8 days

extract_protocol:
RNA was extracted with RNA extraction kit
Total RNA was processed by mRNA enrichment method. MRNA enrichment: the mRNA with Polya tail was enriched by magnetic beads with oligodt. The obtained RNA was fragmented with the interrupt buffer, and the random N6 primers were reverse transcribed, and then the cDNA ⼆ strand was synthesized to form double stranded DNA. The ends of the synthesized double stranded DNA were flattened and phosphorylated at the 5 'end, the 3' end formed a protruding "a" sticky end, and then connected to a bubbly joint with protruding "t" at the 3 'end. The ligation products were amplified by PCR with specific primers. The PCR product was thermally denatured into a single strand, and then the single strand DNA was cyclized with ⼀ segment bridge primers to obtain a single strand circular DNA library. The constructed library was qualified for quality inspection and sequenced (BGI MGI2000).

treatment_protocol: Two replicates were exposure to NEOs, OPEs, SPAs and their metabolites for 8 days

value: Human embryonic stem cells

tag: growth protocol

value: Monolayer differentiation

value: TPHP for 8 days


title: TPHP-S9-2-1

address: 双清路18号林业大学北门

value: TPHP+S9 for 8 days


title: SK-IMZ-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
SK_IMZ_A


title: TPHP-S9-1-1

address: 双清路18号林业大学北门


title: TPHP-1-1

address: 双清路18号林业大学北门


title: TEP-2-1

address: 双清路18号林业大学北门

value: TEP for 8 days


title: TEP-1-1

address: 双清路18号林业大学北门


title: TDCIPP-S9-1-1

address: 双清路18号林业大学北门

value: TDCIPP+S9 for 8 days


title: TDCIPP-2-1

address: 双清路18号林业大学北门

value: TDCIPP for 8 days


title: TDCIPP-S9-2-1

address: 双清路18号林业大学北门


title: TDCIPP-1-1

address: 双清路18号林业大学北门


title: TEP-S9-1-1

address: 双清路18号林业大学北门

value: TEP+S9 for 8 days


title: TEP-S9-2-1

address: 双清路18号林业大学北门


title: TBHQ-1-1

address: 双清路18号林业大学北门

value: TBHQ for 8 days


title: TBHQ-2-1

address: 双清路18号林业大学北门

value: WT


title: IMI-2-1

address: 双清路18号林业大学北门

value: IMI for 8 days


title: IMI-S9-1-1

address: 双清路18号林业大学北门

value: IMI+S9 for 8 days


title: IMI-S9-2-1

address: 双清路18号林业大学北门


title: DTBP-2-1

address: 双清路18号林业大学北门

value: DTBP for 8 days


title: DTBP-1-1

address: 双清路18号林业大学北门


title: DMSO-S9-2-1

address: 双清路18号林业大学北门

value: DMSO+S9 for 8 days


title: DMSO-S9-1-1

address: 双清路18号林业大学北门


title: Control_S9

city: Nice

first: Minoo

last: Rassoulzadegan

address: parc Valrose

department: Institut de Biologie Valrose: iBV

country: France

institute: Nice Sophia Antipolis

description: DNA/RNA hybrids

library_source: other

data_processing:
low-quality reads and adapter sequences were trimmed using Trimmomatic version 0.39 (Bolger et al., 2014) which involved removing 12 nucleotides from the 5′ end of each read and bases with a Phred score lower than 20 from both 5′ and 3′ ends. A minimum threshold of 35 bps was set for the reads after trimming.
Trimmed reads were aligned to the reference genome (hg38) using Hisat2 (M. Pertea et al., 2016) with the command:  ‘hisat2 –dta –rna-strandness’ .
Genome-guided transcriptome assembly was performed using StringTie version 2.1.1
Gene expression quantification was conducted using HTSeq-count
Differential gene expression analysis was performed using DESeq2 (Love et al., 2014) version 1.36.0.
Assembly: hg38
Supplementary files format and content: TSV file of raw counts
Supplementary files format and content: GTF file of transcriptome

molecule: other

source_name: Blood

extract_protocol:
After the enzymatic removal of proteins, total nucleic acids were isolated, and DNA and RNA were fractionated using the standard TRIzolTM protocol (Rio et al., 2010). The nucleic acid fractions from the aqueous phase (RNA) and chloroform-water interphase were ethanol-precipitated separately. These fractions were then re-fractionated through Zymo- SpinTM columns (ZYMO-RESEARCH CORP, Irvine, CA, USA) and eluted or further purified via chloroform extraction. Ethanol precipitated interface materials underwent overnight incubation at 56°C in a buffer containing 20 mM Tris (pH 8), 50 mM EDTA, 0.5% SDS, 20 µM dithiothreitol, and 400 µg/mL Proteinase K. Free RNA was separated, and DNA/RNA hybrids were further purified following DNase digestion and additional purification using Zymo-SpinTM columns (ZYMO-RESEARCH CORP, Irvine, CA, USA). Extracts were treated with RNase (to remove all RNAs), RNaseH (to remove only DNA-RNA hybrids), and DNase (to remove all DNA fragments). Following the enzymatic removal of proteins, total nucleic acids were fractionated into RNA and DNA-bound RNA.
RNA was recovered  from blood samples after DNase digestion with amounts from 10 to 100 ng. High-throughput sequencing was performed on the Illumina HiSeq 2500 or MiSeq platform (Eurofins Medigenomix GmbH, Ebersberg, Germany) (Rassoulzadegan et al., 2021). RNA libraries were prepared from biological replicates of DNA-bound RNA fractions from the autistic patients.

value: Blood

value: Control


title: Control_S8

description: DNA/RNA hybrids


title: NSC-CTRL-A-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
NSC_CTRL_A

value: Blastocyst

value: neural stem cells

value: 0.1% DMSO


title: DMSO-2-1

address: 双清路18号林业大学北门

value: Human embryonic stem cells

value: Monolayer differentiation

value: DMSO for 8 days


title: DMSO-1-1

address: 双清路18号林业大学北门


title: SK-IMZ-B-1

address: 双清路18号林业大学北门

description:
NSC_core_table_gene.xls
SK_IMZ_B

value: Brain

value: SK-N-SH

value: human neuroblastoma

value: IMZ 1 μM


title: Control_S7

description: DNA/RNA hybrids


title: DG-1-1

address: 双清路18号林业大学北门

value: WT

value: DG for 8 days


title: DG-2-1

address: 双清路18号林业大学北门


title: Autism_S3

description: DNA/RNA hybrids

value: Patient


title: Autism_S5

description: DNA/RNA hybrids


title: D0-2-1

address: 双清路18号林业大学北门

value: No treatment


title: Autism_S2

description: DNA/RNA hybrids


title: CYC-S9-2-1

address: 双清路18号林业大学北门

value: CYC+S9 for 8 days


title: D0-1-1

address: 双清路18号林业大学北门


title: Autism_S1

description: DNA/RNA hybrids

value: Blood


title: CYC-S9-1-1

address: 双清路18号林业大学北门


title: Autism_S6

description: DNA/RNA hybrids


title: extr3

city: Jinan

first: Xin

last: Zhang

state: Shandong

address: 107 Wenhua Xi Road

institute: Qilu Hospital, Shandong University

description:
SW480 cells treated with Fn.
extr1(raw)

data_processing:
Unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12); (2) number of base pairs in the stem region of the predicted hairpin (≥16); (3) cutoff of free energy (kCal/mol ≤-15); (4) length of hairpin (up and down stems + terminal loop ≥50); (5) length of hairpin loop (≤200); (6) number of nucleotides in one bulge in mature region (≤4); (7) number of biased errors in one bulge in mature region (≤2); (8) number of biased bulges in mature region (≤2); (9) number of errors in mature region (≤4); (10) number of base pairs in the mature region of the predicted hairpin (≥12); and (11) percent of mature in stem (≥80).
Assembly: Ensembl101
Supplementary files format and content: processed_data.xlsx: Excel file includes raw counts.

source_name: SW480 exosomes

growth_protocol: SW480 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum in a humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from exosomes of cell culture by Trizol LS reagent (Invitrogen).
RNA libraries for RNA-seq were prepared using TruSeq Small RNA Sample Preparation Kit following manufacturer's protocols.

treatment_protocol: SW480 cells were cocultured with Fusobacterium nucleatum or PBS.

value: Colorectal cancer cells

tag: sample type

value: Exosomes

value: Fusobacterium nucleatum infection


title: extr2

description:
SW480 cells treated with Fn.
extr1(raw)


title: IMI-1-1

address: 双清路18号林业大学北门

value: IMI for 8 days


title: CYC-2-1

address: 双清路18号林业大学北门

value: Human embryonic stem cells

value: CYC for 8 days


title: excl2

description:
SW480 cells treated with PBS.
excl2(raw)

value: PBS


title: Eef1g-cKO leptotene and zygotene_rep2

first: Jianze

last: Xu

address: Jinan

institute: Shangdong university

description: Library name: Sample 4

data_processing:
The constructed Ribo-seq libraries were subjected to high-throughput sequencing on the Illumina NovaSeq X Plus platform using a paired-end 150 bp (PE150) strategy. This sequencing strategy, originally designed for small RNA libraries, ensures sufficient coverage and compatibility with ribosome-protected fragment profiling.                                                                                Raw reads were first trimmed using cutadapt with the parameters -j 20 --trim-n --match-read-wildcards -u 3 -n 4 -a AGATCGGAAGAGCACACGTCTG -a AAAAAAAA -a GAACTCCAGTCAC. The trimmed reads were sequentially mapped to mouse or human rRNA sequences (mm10/hg38) using Bowtie with parameters –seedlen=23, and rRNA-aligned reads were discarded. The remaining reads were aligned to the transcriptome (mm10/hg38) using STAR with the parameters –outFilterMismatchNmax 2 –outFilterMultimapNmax 20 –outFilterMatchNmin 16 –alignEndsType EndToEnd. Ribosome profiling (Ribo-seq) data were analyzed using RiboMiner with the code available at https://github.com/xryanglab/RiboMiner.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw FPKM for each Sample
Library strategy: Ribo-Seq

source_name: testis

extract_protocol:
spermatocytes were lysed using RPF lysis buffer (1×, NeoRibo QEZ-seq kit, Cat. R1024L) supplemented with cycloheximide to stabilize ribosome–mRNA complexes. Homogenates were clarified by centrifugation at 12,000 rpm for 10 min at 4 °C. The supernatant containing polysomes was treated with RNase I to digest unprotected mRNA regions, generating ribosome-protected fragments (RPFs). Digestion was stopped by the addition of an RNase inhibitor. RPFs were extracted using TRIzol reagent, followed by isopropanol precipitation, ethanol washing, and resuspension in RNase-free water. The quality and concentration of RNA were assessed by Nanodrop/Qubit and integrity verified by Bioanalyzer or polyacrylamide gel electrophoresis. RPFs were size-selected (26–34 nt) on a 15% polyacrylamide TBE–Urea gel, excised, and eluted for subsequent library preparation.
Ribosome profiling was carried out using the QEZ-seq kit (Hangzhou NeoRibo Biotechnology Co., Ltd., Cat. R1024L) following the manufacturer’s instructions. The QEZ-seq workflow is based on an advanced ribosome footprinting protocol that enables high-resolution mapping of ribosome-protected mRNA fragments, as previously described (Nature Structural & Molecular Biology, 30, 1816–1825, 2023). In brief, cells were lysed under conditions that preserve polysomes, and ribosome–mRNA complexes were digested with RNase I to generate ribosome-protected fragments (RPFs). The fragments were then purified, dephosphorylated, ligated to adaptors, and converted into cDNA libraries according to the QEZ-seq protocol. The resulting libraries were quantified, pooled, and sequenced on an Illumina platform.

tag: tissue

value: testis

value: Leptotene and zygotene spermatocytes


title: extr1

description:
SW480 cells treated with Fn.
extr1(raw)


title: Eef1g-cKO leptotene and zygotene_rep1

description: Library name: Sample 3


title: excl3

description:
SW480 cells treated with PBS.
excl3(raw)


title: BHT-COOH-2-1

address: 双清路18号林业大学北门

value: Monolayer differentiation

value: BHT_COOH for 8 days


title: CYC-1-1

address: 双清路18号林业大学北门

value: WT


title: FnsH6

source_name: serum exosomes

extract_protocol:
RNA was harvested using Trizol LS.
RNA libraries for RNA-seq were prepared using TruSeq Small RNA Sample Preparation Kit following manufacturer's protocols.

value: serum

value: exosomes

tag: gender

value: Female

value: colorectal cancer (CRC)

tag: tnm stage

value: II

tag: f. nucleatum abundance

value: High abundance


title: Control leptotene and zygotene_rep2

description: Library name: Sample 2

value: Wild type


title: FnsH5

value: Male

value: IV


title: Control leptotene and zygotene_rep1

description: Library name: Sample 1


title: FnsH3

value: III


title: BHT-COOH-1-1

address: 双清路18号林业大学北门

tag: cell line

value: Human embryonic stem cells

tag: treatment


title: FnsH4


title: BHT-CHO-2-1

address: 双清路18号林业大学北门

tag: cell type

tag: genotype

value: BHT_CHO for 8 days


title: FnsH2


title: FnsH1


title: Sample_02_03

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

country: Germany

institute: University Hospital Essen

data_processing:
scRNA-seq: cwl-runner v.2.0 was used to obtain counts
Samples are tagged with sample tag (see feature Readme)
Assembly: hg38
Supplementary files format and content: barcodes, features, matrix contain the raw unfiltered data as result from Rhapsodys cwl runner v2.0
Supplementary files format and content: rds file contains the filtered cells already as Seurat object, feature_readme contains the single sample_tag assignment

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
Library was performed according to the manufacter’s instructions (see also M&M).

treatment_protocol: iPSC-derived lung organoids were cultured under standard conditions, irradiated and total RNA was isolated prior RNAseq, for scRNAseq lung organoids were enzymatically digested and sc analyses were perfomed (non-irradiated and irradiated condition) and

value: lung

value: iPSC

value: various lung cell types

value: unknown

value: control/RT


title: BHT-CHO-1-1

address: 双清路18号林业大学北门

value: WT

value: Monolayer differentiation


title: WT_2

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

description:
Ten oocytes
Bulk RNA-seq

data_processing:
The RNA-seq data were first subjected to adaptor trimming and low-quality read filtering with flexbar (version 2.5).
The trimmed paired-end reads were then aligned to the mouse reference genome (mm10) by STAR (version 2.7.10b) under the parameters: -outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 6 --alignSJDBoverhangMin 1 --outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonicalUnannotated
HTSeq (v0.13.5) was employed for gene expression quantification.
Assembly: mm10
Supplementary files format and content: txt, gene expression read counts.

source_name: Oocyte

extract_protocol:
Each sample is lysed using a 2 µL lysis buffer with 0.2% TritonX-100 and 40 U/mL Recombinant RNase Inhibitor, which disrupts cell membranes to release RNA and other cellular contents while preventing RNA degradation.
Poly(A)-tailed RNA molecules in cells were processed using the Smart-seq2 protocol. Lysis of each sample in a specialized buffer, followed by reverse transcription and cDNA amplification for 16 cycles. Tagmentation with Tn5 enzyme mix and PCR was employed to build sequencing libraries, which were then amplified and purified. Library quality was assessed using PerkinElmer LabChip GX Touch.

value: Oocyte

tag: Stage

value: MII

value: young

value: siCtrl


title: KD_1

description:
Ten oocytes
Bulk RNA-seq

value: siPlat


title: FnsL5

value: serum

value: exosomes

value: Female

value: colorectal cancer (CRC)

value: Not detected


title: BHT-2-1

address: 双清路18号林业大学北门

value: Human embryonic stem cells

value: BHT for 8 days


title: WT_1

description:
Ten oocytes
Bulk RNA-seq


title: BHT-1-1

address: 双清路18号林业大学北门


title: excl1

description:
SW480 cells treated with PBS.
excl1(raw)

value: Colorectal cancer cells

value: Exosomes

value: PBS


title: FnsL4

value: Male

value: II


title: FnsL3


title: BHA-2-1

address: 双清路18号林业大学北门

value: WT

value: Monolayer differentiation

value: BHA for 8 days


title: WT_Tac1a_Mnase 10 min R1

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

country: Canada

institute: Universite de Montreal

description: Library name: WT_Tac1a_Mnase 10 min R1

data_processing:
Sequencing reads were filtered with fastp version 0.23.2
Sequences were trimmed to remove adapters using TRIMMOMATIC with options “TRAILING:30”. Filtered reads were mapped to the reference genome sequence of strain SC5314 with STAR version 2.7.9a
Reads were mapped to the C. auris genome using Bowtie2 with “-q --phred33 --no-unal” options. Peaks were determined using MACS2 algorithm with options “-BAM -nomodel-extsize 200-keep-dup all.”.
Assembly: Reference genome of the C. auris B8441strain were used (http://www.candidagenome.org/download/sequence/C_auris_B8441/).
Supplementary files format and content: CheC-seq processed data files contain the raw counts for each sequencing experiment.

organism: Candidozyma auris

source_name: Yeast cells

growth_protocol: Overnight cultures of C. auris MNase-tagged and Free MNase strains were diluted in 50 ml of YEPD to an initial OD600 of 0.2 and incubated at 37°C until reaching an OD600 of 0.7–0.8.

extract_protocol:
DNA was purified using the MasterPure Yeast DNA Purification Kit (Epicentre) following the manufacturer’s instructions and resuspended in 50µl of 10 mM Tris-HCl buffer (pH 8.0)
The NEBNext UltraTM II RNA Library Prep Kit for Illumina was used to construct the RNA-seq library. For the ChEC-seq, sequencing libraries were prepared using the KAPA HyperPrep Kits.

treatment_protocol: Cells were grown exponentially in YPD medium to reach OD600 of 0.7–0.8.

value: Yeast cells

value: Grown exponentially in YPD medium


title: WT_Mnase-free_Tac1a 10 min R2

description: Library name: WT_Mnase-free_Tac1a 10 min R2


title: aged_1-59

description:
This Sample represents 59 single aged oocytes.
Smart-seq2

value: Oocyte

value: MII

value: aged


title: young_1-35

description:
This Sample represents 35 single young oocytes.
Smart-seq2

value: young


title: WT_Tac1a_Mnase 10 min R2

description: Library name: WT_Tac1a_Mnase 10 min R2


title: FnsL6

value: serum

value: exosomes

value: colorectal cancer (CRC)

value: Not detected


title: BHA-1-1

address: 双清路18号林业大学北门

value: Human embryonic stem cells


title: WT_Mnase-free_Tac1a 10 min R1

description: Library name: WT_Mnase-free_Tac1a 10 min R1


title: AO-2246-2-1

address: 双清路18号林业大学北门

value: AO_2246 for 8 days


title: FnsL2

value: Male


title: WT_Tac1b_Mnase 60 min R2

description: Library name: WT_Tac1b_Mnase 60 min R2


title: AO-2246-1-1

address: 双清路18号林业大学北门


title: Mouse CS-CON4

city: Guangzhou

first: Zhandong

address: No. 9, Xingdao Ring North Road, International Biomedical Island

institute: Guangzhou National Laboratory

description: Library name: SAMN50839311

data_processing:
edgeR
Assembly: HISAT2, Bowtie2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Lung

growth_protocol: All animals were kept under a SPF condition and free to water and food.

extract_protocol:
RNA was harvested using TRIzol® Reagent (Invitrogen).
The mRNA was isolated from the total RNA via Magnetic beads with Oligo dt and randomly broken into 300-bp fragments using fragmentation buffer. These small mRNA fragments were reversely transcribed into cDNA, followed by fragment purification and sorting, PCR amplification and library construction.

treatment_protocol: All animals were exposed to cigarette smoking, meanwhile mice in the CS-Chol group were fed with cholesterol.

value: Lung

tag: Sex

tag: time

value: 30 wekks

value: cigarette smoking exposure


title: FnsL1

tag: age

value: III


title: KD_2

description:
Ten oocytes
Bulk RNA-seq

value: siPlat


title: Sample_05_06_07_08

value: lung

value: iPSC

value: various lung cell types

value: unknown

value: control/RT


title: Mouse CS-CON3

description: Library name: SAMN50839308

value: WT


title: sctrl3

description:
SW480 cells treated with PBS.
sctrl3(raw)

extract_protocol:
RNA was harvested using Trizol. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Small RNA Sample Preparation Kit following manufacturer's protocols.

value: Colorectal cancer cells

value: PBS


title: AO168-O-2-1

address: 双清路18号林业大学北门

value: Monolayer differentiation

value: AO168_O for 8 days


title: WT_Tac1b_Mnase 60 min R1

description: Library name: WT_Tac1b_Mnase 60 min R1

value: Yeast cells

value: Grown exponentially in YPD medium


title: Mouse CS-CON2

description: Library name: SAMN50839307

value: Lung

value: Male


title: sctrl2

description:
SW480 cells treated with PBS.
sctrl2(raw)


title: WT_Tac1b_Mnase 10 min R1

description: Library name: WT_Tac1b_Mnase 10 min R1


title: Mouse CS-CON1

description: Library name: SAMN50839305

value: 30 wekks

value: cigarette smoking exposure


title: ACE-S9-2-1

address: 双清路18号林业大学北门

value: Human embryonic stem cells

value: ACE+S9 for 8 days


title: AO168-O-1-1

address: 双清路18号林业大学北门


title: sctrl1

description:
SW480 cells treated with PBS.
sctrl1(raw)


title: Mouse CS-Chol4

description: Library name: SAMN50839293

value: cigarette smoking exposure and high-cholesterol diet


title: Mouse CS-Chol3

description: Library name: SAMN50839172


title: str3

description:
SW480 cells treated with Fn.
str3(raw)

value: Fusobacterium nucleatum infection


title: WT_Mnase-free 60 min R1

description: Library name: WT_Mnase-free 60 min R1


title: WT_Mnase-free 10 min R2

description: Library name: WT_Mnase-free 10 min R2


title: ACE-2-1

address: 双清路18号林业大学北门

value: ACE for 8 days


title: WT_Mnase-free 60 min R2

description: Library name: WT_Mnase-free 60 min R2


title: ACE-S9-1-1

address: 双清路18号林业大学北门


title: Mouse CS-Chol2

description: Library name: SAMN50839149


title: str1

description:
SW480 cells treated with Fn.
str1(raw)


title: ACE-1-1

address: 双清路18号林业大学北门


title: WT_Mnase-free 10 min R1

description: Library name: WT_Mnase-free 10 min R1


title: Mouse CS-Chol1

description: Library name: SAMN50839016


title: MPE_A_23

status: Public on Sep 12 2025

type: genomic

city: Hamburg

first: Karoline

last: Hack

address: Martinistraße 52

department: Children's Cancer Center Hamburg

institute: University Medical Center Hamburg-Eppendorf

description: recurred myxopapillary ependymoma subtype A

hyb_protocol: For subsequent bisulfite conversion, 100-500 ng of DNA were input to the EZ DNA Methylation Kit (Zymo Research). DNA samples were cleaned utilizing the DNA Clean & Concentrator-5 Kit (Zymo Research) and restored by the Infinium HD FFPE DNA Restore Kit (Illumina).

scan_protocol: The iScan system was used in combination with the Infinium HumanMethylation450 or MethylationEPIC BeadChip Kit (Illumina) to detect the methylation status of 450,000 or 850,000 genome-wide CpG sites, respectively.

data_processing: The package minfi v1.52.1 was used to preprocess and normalize Illumina methylation array data (preprocessIllumina function) and calculate β-values in R programming language. The intersection of detected CpGs across all arrays was used for further analyses. SNP-associated CpGs, cross-hybridising probes as well as CpGs located on sex-chromosomes were excluded from analysis.

label: Cy3 and Cy5

source_name: Frozen

label_protocol: Standard Illumina Protocol

extract_protocol: For the generation of DNA methylation array data, the Maxwell® FFPE DNA Kit (Promega) was used for the extraction of genomic DNA from FFPE tissues.

tag: patient number (hack et al. 2025)

value: Frozen

tag: age at diagnosis

tag: localization

value: not annotated

tag: radiation therapy prior to resection


title: MPE_A_21

source_name: FFPE

value: FFPE

value: Spinal cord, S1/2

value: no


title: MPE_A_22

description: primary myxopapillary ependymoma subtype A

value: Spinal cord, L3-5


title: MPE_A_19

value: Spinal cord, L4-S1

value: yes


title: MPE_A_18

value: Spinal cord, L5


title: WT_Tac1b_Mnase 10 min R2

description: Library name: WT_Tac1b_Mnase 10 min R2

value: Yeast cells

value: Grown exponentially in YPD medium


title: MPE_A_16

value: Spinal cord, L4-S3


title: MPE_A_20

value: Spinal cord, lumbar


title: MPE_A_17

value: Spinal cord, T10


title: MPE_A_15

value: Spinal cord, L1-S1


title: MPE_A_13

value: Spinal cord, S1


title: MPE_A_14

value: Spinal cord, L1-S2


title: MPE_A_12

value: Spinal cord, L3-S1


title: MPE_A_10

value: Spinal cord, L2-4


title: MPE_A_11

value: FFPE


title: MPE_A_9

value: Spinal cord, L5-S1


title: str2

description:
SW480 cells treated with Fn.
str2(raw)

value: Colorectal cancer cells

value: Fusobacterium nucleatum infection


title: MPE_A_7

value: Spinal cord, T5-10

value: no


title: MPE_A_8

value: Spinal cord, T11-L1


title: MPE_A_5

value: Spinal cord, L5


title: MPE_A_6


title: MPE_A_4


title: NCI-H838 xenograft tumor, PD, PRT3789 (s.c., Day 0 + 3) + Nab-paclitaxel (i.v., Day 0), rep3

city: Wilmington

first: Michael

last: Hulse

state: DE

address: 175 Innovation Blvd

institute: Prelude Therapeutics

description:
Library name: G6_42520
Column name in PLX149655_assay_data.csv: G6_42520

data_processing:
FASTQ files were processed using the nf-core/rnaseq pipeline (v3.17.0) (auto strandedness).
Adapter sequences were removed with Trim Galore.
Reads were aligned with STAR to GRCh38 (NCBI, p.14, release 110) and quantified to gene counts using RSEM.
Downsteam analysis was performed using Pluto Bio (https://pluto.bio).
Assembly: GRCh38 (NCBI, p.14, release 110)
Supplementary files format and content: comma-delimited text file includes raw counts for each Sample

source_name: NCI-H838 xenograft tumor

growth_protocol: The NCI-H838-#5 tumor cells were maintained in vitro in RPMI-1640 medium supplemented with 10 percent fetal bovine serum at 37 degrees Celsius in a humidified atmosphere containing 5 percent CO2 in air. Cells in the exponential growth phase were harvested and counted using a cell counter prior to inoculation. Each mouse was inoculated subcutaneously in the right front flank region with 5 × 10^6 NCI-H838-#5 tumor cells in 0.1 mL of PBS mixed 1:1 with Matrigel to promote tumor development. Randomization was initiated when the mean tumor volume reached approximately 250 cubic millimeters. A total of 18 mice were enrolled and randomly allocated to six study groups (n=3 per group) using the Matched distribution method in StudyDirector software, version 3.1.399.19. The date of randomization was designated as Day 0.

extract_protocol:
At 120 hours post–first dose, tumors were excised, flash-frozen in liquid nitrogen, and processed by Crown Bioscience for RNA extraction. RNA quality was assessed prior to library construction to ensure suitability for sequencing.
High-quality RNA was enriched for mRNA, fragmented, and reverse transcribed into cDNA. Strand-specific libraries were prepared, adapter-ligated, PCR-amplified, and quantified. Libraries were sequenced on an Illumina platform to generate 2 × 150 bp paired-end reads.

value: NCI-H838 xenograft tumor

tag: readout

value: PD


title: NCI-H838 xenograft tumor, Efficacy, PRT3789 (s.c., Day 0 + 3), rep1

description:
Library name: G2_25354
Column name in PLX149655_assay_data.csv: G2_25354

tag: tissue

value: Efficacy


title: NCI-H838 xenograft tumor, Efficacy, PRT3789 (s.c., Day 0 + 3) + Docetaxel (i.v., Day 0), rep2

description:
Library name: G8_25397
Column name in PLX149655_assay_data.csv: G8_25397


title: NCI-H838 xenograft tumor, Efficacy, Docetaxel (i.v., Day 0), rep2

description:
Library name: G5_25394
Column name in PLX149655_assay_data.csv: G5_25394

value: Docetaxel (i.v., Day 0)


title: NCI-H838 xenograft tumor, Efficacy, Vehicle (s.c., Day 0 + 3) + saline (i.v., Day 0), rep1

description:
Library name: G1_25356
Column name in PLX149655_assay_data.csv: G1_25356


title: NCI-H838 xenograft tumor, Efficacy, Vehicle (s.c., Day 0 + 3) + saline (i.v., Day 0), rep2

description:
Library name: G1_25395
Column name in PLX149655_assay_data.csv: G1_25395


title: NCI-H838 xenograft tumor, PD, PRT3789 (s.c., Day 0 + 3) + Nab-paclitaxel (i.v., Day 0), rep1

description:
Library name: G6_42510
Column name in PLX149655_assay_data.csv: G6_42510


title: NCI-H838 xenograft tumor, Efficacy, Docetaxel (i.v., Day 0), rep1

description:
Library name: G5_25367
Column name in PLX149655_assay_data.csv: G5_25367


title: NCI-H838 xenograft tumor, PD, PRT3789 (s.c., Day 0 + 3) + Nab-paclitaxel (i.v., Day 0), rep2

description:
Library name: G6_42518
Column name in PLX149655_assay_data.csv: G6_42518


title: NCI-H838 xenograft tumor, Efficacy, PRT3789 (s.c., Day 0 + 3), rep2

description:
Library name: G2_25379
Column name in PLX149655_assay_data.csv: G2_25379


title: NCI-H838 xenograft tumor, PD, PRT3789 (s.c., Day 0 + 3) + Docetaxel (i.v., Day 0), rep2

description:
Library name: G5_42521
Column name in PLX149655_assay_data.csv: G5_42521


title: NCI-H838 xenograft tumor, PD, Nab-paclitaxel (i.v., Day 0), rep3

description:
Library name: G4_42526
Column name in PLX149655_assay_data.csv: G4_42526

value: Nab-paclitaxel (i.v., Day 0)


title: NCI-H838 xenograft tumor, PD, Nab-paclitaxel (i.v., Day 0), rep1

description:
Library name: G4_42511
Column name in PLX149655_assay_data.csv: G4_42511


title: NCI-H838 xenograft tumor, PD, Nab-paclitaxel (i.v., Day 0), rep2

description:
Library name: G4_42523
Column name in PLX149655_assay_data.csv: G4_42523


title: NCI-H838 xenograft tumor, PD, Docetaxel (i.v., Day 0), rep3

description:
Library name: G3_42514
Column name in PLX149655_assay_data.csv: G3_42514


title: NCI-H838 xenograft tumor, PD, PRT3789 (s.c., Day 0 + 3) + Docetaxel (i.v., Day 0), rep1

description:
Library name: G5_42517
Column name in PLX149655_assay_data.csv: G5_42517


title: NCI-H838 xenograft tumor, PD, PRT3789 (s.c., Day 0 + 3) + Docetaxel (i.v., Day 0), rep3

description:
Library name: G5_42529
Column name in PLX149655_assay_data.csv: G5_42529


title: NCI-H838 xenograft tumor, PD, PRT3789 (s.c., Day 0 + 3), rep2

description:
Library name: G2_42512
Column name in PLX149655_assay_data.csv: G2_42512


title: NCI-H838 xenograft tumor, PD, PRT3789 (s.c., Day 0 + 3), rep3

description:
Library name: G2_42519
Column name in PLX149655_assay_data.csv: G2_42519


title: NCI-H838 xenograft tumor, PD, Docetaxel (i.v., Day 0), rep2

description:
Library name: G3_42513
Column name in PLX149655_assay_data.csv: G3_42513


title: NCI-H838 xenograft tumor, PD, PRT3789 (s.c., Day 0 + 3), rep1

description:
Library name: G2_42507
Column name in PLX149655_assay_data.csv: G2_42507


title: NCI-H838 xenograft tumor, PD, Vehicle (s.c., Day 0 + 3) + saline (i.v., Day 0), rep2

description:
Library name: G1_42522
Column name in PLX149655_assay_data.csv: G1_42522


title: NCI-H838 xenograft tumor, PD, Docetaxel (i.v., Day 0), rep1

description:
Library name: G3_42506
Column name in PLX149655_assay_data.csv: G3_42506


title: NCI-H838 xenograft tumor, PD, Vehicle (s.c., Day 0 + 3) + saline (i.v., Day 0), rep1

description:
Library name: G1_42508
Column name in PLX149655_assay_data.csv: G1_42508


title: NCI-H838 xenograft tumor, Efficacy, PRT3789 (s.c., Day 0 + 3) + Docetaxel (i.v., Day 0), rep1

description:
Library name: G8_25389
Column name in PLX149655_assay_data.csv: G8_25389


title: hTERT-immortalized PDAC CAFs, monoculture, mRNA, Pool C4

city: South San Francisco

first: Elysia

middle: Cecilia

last: Saputra

state: CA

address: 213 E Grand Ave

department: Data, AI, and Genome Sciences

institute: Merck & Co., Inc.

description:
Library name: monoculture_poolC4_GEX
mRNA

data_processing:
The demultiplexing of sequencing reads, gene counting, and generation of gene expression matrices were performed using the 10X Genomics Cell Ranger v7.0.1 software. Quality control, normalization, library integration, identification of non-perturbed cells, label transfer, and subtype identification were performed using Seurat 4.1.1.
Assembly: Homo sapiens hg38
Supplementary files format and content: RDS files

source_name: fibroblast

growth_protocol: hTERT-immortalized CAF cell lines were suspended in 20mL of FBM with polybrene (16 ug/mL), and then aliquoted to 6-well plates.

extract_protocol:
After aspirating media, 350uL accutase is added to the cell culture, followed by 350uL FBM when the cells have detached. Then, cells are spun (300g, 5 minutes) and resuspended in 2% FBS RPMI to get ~2000/uL. The cells were then loaded to 10X 5'HT Chip based on 10X protocol and run in Chromium X. Afterwards, cDNA amplification was performed following 10X protocol. Libraries were quantified using qubit and sequenced using S4 Illumina flow cell.
Library construction was performed according to the 10X 5' CRISPR protocol following the manufacturer's instruction.

treatment_protocol: 500uL of lentivirus/guide was added to the solution to a final polybrene concentration of 8ug/mL. Then, the media was replaced, and then 1mL of 1.5ug/mL puromycin was added to each well to a final concentration of 0.5ug/mL. After adding 0.5mL accutase and 0.5mL media, the cells were split in 6-well plates (400uL cells/well). Then, 600uL media and 1ug/mL puromycin was added to a final concentration of 0.5ug/mL. The solution was then replaced with fresh FBM without puromycin. To set up the monocultures and cocultures, media was first aspirated, and 500uL accutase was added. After the cells have detached, 500uL media was added. After that, 1e5 of the perturbed CAF cells were added to each well in 12-well plates. To set up the monocultures, 1mL of 2% FBS RPMI was added. To set up the cocultures, 1mL of tumor cells were added. The cultures were incubated for 2 days.

value: fibroblast

tag: batch


title: hTERT-immortalized PDAC CAFs, monoculture, sgRNA, Pool C3

description:
Library name: monoculture_poolC3_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, monoculture, sgRNA, Pool C4

description:
Library name: monoculture_poolC4_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, monoculture, mRNA, Pool C3

description:
Library name: monoculture_poolC3_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, monoculture, sgRNA, Pool B3

description:
Library name: monoculture_poolB3_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, monoculture, mRNA, Pool A3

description:
Library name: monoculture_poolA3_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, monoculture, mRNA, Pool B3

description:
Library name: monoculture_poolB3_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool C9

description:
Library name: coculture_poolC9_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, monoculture, sgRNA, Pool A4

description:
Library name: monoculture_poolA4_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, monoculture, sgRNA, Pool A3

description:
Library name: monoculture_poolA3_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, monoculture, mRNA, Pool B4

description:
Library name: monoculture_poolB4_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, monoculture, sgRNA, Pool B4

description:
Library name: monoculture_poolB4_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool C15

description:
Library name: coculture_poolC15_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool C9

description:
Library name: coculture_poolC9_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool C14

description:
Library name: coculture_poolC14_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool C13

description:
Library name: coculture_poolC13_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool C16

description:
Library name: coculture_poolC16_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool C13

description:
Library name: coculture_poolC13_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool C10

description:
Library name: coculture_poolC10_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool C8

description:
Library name: coculture_poolC8_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, monoculture, mRNA, Pool A4

description:
Library name: monoculture_poolA4_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool C10

description:
Library name: coculture_poolC10_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool C8

description:
Library name: coculture_poolC8_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool C15

description:
Library name: coculture_poolC15_CRISPR
sgRNA


title: NCI-H838 xenograft tumor, PD, Vehicle (s.c., Day 0 + 3) + saline (i.v., Day 0), rep3

description:
Library name: G1_42528
Column name in PLX149655_assay_data.csv: G1_42528


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool C6

description:
Library name: coculture_poolC6_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool C7

description:
Library name: coculture_poolC7_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool C5

description:
Library name: coculture_poolC5_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool C6

description:
Library name: coculture_poolC6_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool C5

description:
Library name: coculture_poolC5_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool C16

description:
Library name: coculture_poolC16_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool C12

description:
Library name: coculture_poolC12_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool B9

description:
Library name: coculture_poolB9_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool C11

description:
Library name: coculture_poolC11_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool B9

description:
Library name: coculture_poolB9_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool C14

description:
Library name: coculture_poolC14_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool C11

description:
Library name: coculture_poolC11_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool B8

description:
Library name: coculture_poolB8_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool B8

description:
Library name: coculture_poolB8_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool B6

description:
Library name: coculture_poolB6_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool B5

description:
Library name: coculture_poolB5_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool B6

description:
Library name: coculture_poolB6_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool B5

description:
Library name: coculture_poolB5_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool B14

description:
Library name: coculture_poolB14_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool B14

description:
Library name: coculture_poolB14_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool B13

description:
Library name: coculture_poolB13_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool B12

description:
Library name: coculture_poolB12_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool C7

description:
Library name: coculture_poolC7_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool B13

description:
Library name: coculture_poolB13_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool B12

description:
Library name: coculture_poolB12_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool A8

description:
Library name: coculture_poolA8_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool A7

description:
Library name: coculture_poolA7_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool A7

description:
Library name: coculture_poolA7_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool A8

description:
Library name: coculture_poolA8_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool A5

description:
Library name: coculture_poolA5_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool A6

description:
Library name: coculture_poolA6_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool C12

description:
Library name: coculture_poolC12_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool A16

description:
Library name: coculture_poolA16_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool A15

description:
Library name: coculture_poolA15_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool A13

description:
Library name: coculture_poolA13_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool A12

description:
Library name: coculture_poolA12_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool A14

description:
Library name: coculture_poolA14_GEX
mRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool A11

description:
Library name: coculture_poolA11_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool A11

description:
Library name: coculture_poolA11_GEX
mRNA