title: mel3

city: Manchester

first: Amaya

last: Viros

address: Wilmslow Road

department: Skin Cancer Ageing

institute: Cancer Research UK

description:
Library name: melanoma3
FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline (version 2.0.1) using default settings and aligning to GRCh38-2020-A
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5: H5 file containing the feature barcode matrix
Supplementary files format and content: aligned_fiducials.jpg: aligned fudicials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the co-ordinates specifiying spots
Library strategy: Spatial Transcriptomics

source_name: Cutaneous melanoma

extract_protocol:
Sections cut from FFPE blocks
Indexed sequencing libraries were prepared from H&E-stained Visium Spatial Gene Expression Slides using the Visium Spatial for FFPE Gene Expression Kit, Human Transcriptome, (10x Genomics, 1000338) according to the manufacturer’s protocol.

value: Cutaneous melanoma


title: ESCFCS Setd1a WT biol rep 2

status: Public on Feb 18 2026

type: SRA

city: Dresden

first: Anna

middle: R

last: Poetsch

address: Tatzberg 47/49

country: Germany

institute: TU Dresden

description:
Library name: Sample 24
Column name in bfx754.mm10.e87.txt: RNA24

library_source: transcriptomic

data_processing:
Reads were mapped to GRCm38/mm10 with GSNAP version 2017-03-17
Read counts extraction and normalization were performed using featureCounts v1.5.2
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Cycling Embryonic Stem Cells

extract_protocol:
Total RNA was isolated with Trizol (Invitrogen) according to the manufacturer's recommendations. 100 μg total RNA was subjected to two rounds of poly(A) selection (Oligotex mRNA Mini Kit; QIAGEN), followed by DNaseI treatment (QIAGEN).
100–200 ng mRNA was fragmented by hydrolysis (5× fragmentation buffer: 200mM Tris acetate, pH8.2, 500mM potassium acetate and 150mM magnesium acetate) at 94°C for 90 s and purified (RNAeasy Minelute Kit; QIAGEN). cDNA was synthesized with 5 μg random hexamers by Superscript III Reverse Transcriptase (Invitrogen). Ds cDNA synthesis was performed in second strand buffer (Invitrogen) according to the manufacturer's recommendations and purified (Minelute Reaction Cleanup Kit; QIAGEN). Strand-specific rRNA depleted ds cDNA profiling was performed with the ScriptSeq kit (cat. no. SS10924) from Illumina, according to the instructions of the manufacturer. rRNA depletion was performed with the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat; cat. no. RZH110424).

tag: cell type

value: Cycling Embryonic Stem Cells

tag: genotype

value: WT

tag: treatment

value: Media with LIF and FCS


title: 103_P11_D04

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

country: USA

institute: National Cancer Institute, NIH

description: Expression_CountValue.tsv,Expression_FPKM.tsv,Expression_TPM.tsv,Mutations.tsv

library_source: transcriptomic single cell

data_processing:
We used GATK Best Practices to call mutations from scRNAseq, bWTS and bWES datasets. Depends on the data there are some modifications in the pipeline. Briefly, after trimming and quality control of reads by FastQ (v0.11.9) and Trim Galore (v0.6.5), raw reads were mapped to the mouse genome (GRCm38, mm10) using STAR (v2.7.3a) in two-pass mode which improves the mapping quality at junction sites. Then Picard (v2.22.3) was used for removing duplicated mapped reads and doing indel realignment and base re-calibration. During base quality recalibration, dbSNP variants were used as known sites. In the next step, HaplotypeCaller (v3.8) was used to call the mutations for every single cell separately in GVCF mode. After that, GenotypeGVCFs was used to call the mutations in a joint mode (as pseudo-bulk). These steps keep specificity and sensitivity of calling mutations high. Afterward, the mutations were annotated using ANNOVAR (v2019.10.24). Following that, mutations that were marked as unknown and non-exonic were filtered out. For further confidence, mouse SNPs/Indels filtration was applied to the VCF files based on normal mouse spleen SNPs in addition to a curated in-house database. Finally, somatic-mutations associated with less than 10 reads in at least 2 cells were filtered out. RSEM (v1.3.2) was used to extract expected counts, TPM and FPKM information.
Assembly: mouse mm10
Supplementary files format and content: tab-delimited text files include expression matrix where rows are samples and columns are genes
Supplementary files format and content: tab-delimited text file include all exonic mutations in the samples

source_name: Tumor #103

extract_protocol: Smart-seq2 (Nature Protocol, 2014, 9: 171)

tag: tissue

value: Melanoma cell line-derived tumor

tag: strain

value: HGF-tg C57BL6

tag: microbiota status

tag: sorting strategy

value: CD45-, CD31-, alive, nucleated cells


title: mel2

country: United Kingdom

description:
Library name: melanoma2
FFPE Spatial transcriptome sequencing

organism: Homo sapiens


title: ESCFCS Setd1a KO Tamoxifen biol rep 1

description:
Library name: Sample 21
Column name in bfx754.mm10.e87.txt: RNA21

value: Setd1a KO


title: ESCFCS Setd1a WT biol rep 1

description:
Library name: Sample 22
Column name in bfx754.mm10.e87.txt: RNA22


title: EpiSC Bod1L WT biol rep 1

description:
Library name: Sample 26
Column name in bfx754.mm10.e87.txt: RNA26

source_name: Epiblast-like Stem Cells

value: Epiblast-like Stem Cells

value: Media with Activin A and FGF2


title: ESCFCS Mll2 WT biol rep 2

description:
Library name: Sample 20
Column name in bfx754.mm10.e87.txt: RNA20


title: PC-3

city: Atlanta

first: Linqi

last: Jin

state: Georgia

address: 1750 Haygood Dr HSRB II, Floor 4 Room S435

department: Biomedical Engineering

institute: Emory University

description:
Library name: Sample 9
10X Genomics

data_processing:
Raw sequencing reads were demultiplexed and aligned to the GRCh28 human genome using the Cell Ranger (v.7.1.0) pipeline from 10x Genomics. UMI counts were quantified per gene per cell to generate a gene-barcode matrix.
Assembly: Human GRCh38
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.tsv.gz.

source_name: 3D bioprinted cardiac tissue

growth_protocol: CMs were differentiated from hiPSCs via WNT inhibition and cultured with CM expansion media in 2D, HUVECs were cultured with EC media in 2D, CM/EC coculture was maintained using a mixture of 90% CM and 10% EC media.

extract_protocol:
For 2D cell culture, ECs and CMs were dissociated using trypsin-EDTA (0.05%, Thermo Fisher) and TrypLE Select 10X at approximately 95% confluency and resuspended in fresh EC media and CM replating media, respectively. For 3D tissue culture, eHT samples were washed with warm PBS (5 min for 3 times), cut into small pieces, and enzymatically digested by incubation with 4 mg/mL collagenase type I (STEMCELL Technologies) and 1 mg/mL DNase I (STEMCELL Technologies) at 37 °C for 20 min, including 10 min with the addition of TrypLE Select 10X. The digested samples were filtered through a 100 µm cell strainer for up to 3 times to remove the remaining hydrogel residues. After the removal of the dissociation media, cells were resuspended in CM replating medium.
The scRNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3’ Kit (v 3.1) and sequenced on a Novaseq S4 flowcell (Illumina, San Diego, CA, USA) to a mean read depth of at least 54,000 total aligned reads per cell.

treatment_protocol: 1) 2D CM/EC monoculture, 2) 3D bioprinted embryonic heart tube coculture (7 days static, 7 days static + 5 days perfusion)

value: 3D bioprinted cardiac tissue

tag: cell line

value: SCVI-15 and GFP-HUVEC

value: cardiomyocytes, endothelial cells, fibroblasts, and blood cells

value: 3D static + perfusion coculture, d20


title: ESCFCS Mll2 KO  Tamoxifen biol rep 2

description:
Library name: Sample 19
Column name in bfx754.mm10.e87.txt: RNA19

value: Mll2 KO


title: 103_P11_D03


title: ESCFCS Mll2 WT biol rep 1

description:
Library name: Sample 18
Column name in bfx754.mm10.e87.txt: RNA18


title: ESCFCS Bod1L WT biol rep 2

description:
Library name: Sample 16
Column name in bfx754.mm10.e87.txt: RNA16


title: ESCFCS Mll2 KO Tamoxifen biol rep 1

description:
Library name: Sample 17
Column name in bfx754.mm10.e87.txt: RNA17


title: ESCFCS Bod1L KO Tamoxifen biol rep 2

description:
Library name: Sample 15
Column name in bfx754.mm10.e87.txt: RNA15

value: Bod1L KO


title: 103_P11_D02


title: PC-2

description:
Library name: Sample 8
10X Genomics


title: ESCFCS Bod1L WT biol rep 1

description:
Library name: Sample 14
Column name in bfx754.mm10.e87.txt: RNA14


title: SC-4

description:
Library name: Sample 6
10X Genomics

value: 3D static coculture, d14


title: PC-1

description:
Library name: Sample 7
10X Genomics


title: 103_P11_D01


title: ESC2i Setd1a WT biol rep 2

description:
Library name: Sample 12
Column name in bfx754.mm10.e87.txt: RNA12

source_name: Naive Embryonic Stem Cells

value: Naive Embryonic Stem Cells

value: Media with LIF, PD0325901 and CT99021


title: SC-3

description:
Library name: Sample 5
10X Genomics

value: WT


title: ESCFCS Bod1L KO Tamoxifen biol rep 1

description:
Library name: Sample 13
Column name in bfx754.mm10.e87.txt: RNA13

value: Cycling Embryonic Stem Cells

value: Media with LIF and FCS


title: ESC2i Setd1a KO Tamoxifen biol rep 2

description:
Library name: Sample 11
Column name in bfx754.mm10.e87.txt: RNA11


title: 103_P11_C12

value: Melanoma cell line-derived tumor

value: HGF-tg C57BL6


title: SC-2

description:
Library name: Sample 4
10X Genomics


title: 103_P11_C11

value: CD45-, CD31-, alive, nucleated cells


title: ESC2i Setd1a WT biol rep 1

description:
Library name: Sample 10
Column name in bfx754.mm10.e87.txt: RNA10


title: ESC2i Mll2 WT biol rep 2

description:
Library name: Sample 8
Column name in bfx754.mm10.e87.txt: RNA8


title: ESC2i Mll2 WT biol rep 1

description:
Library name: Sample 6
Column name in bfx754.mm10.e87.txt: RNA6


title: 103_P11_C10

description: Expression_CountValue.tsv,Expression_FPKM.tsv,Expression_TPM.tsv,Mutations.tsv


title: ESC2i Mll2 KO Tamoxifen biol rep 1

description:
Library name: Sample 5
Column name in bfx754.mm10.e87.txt: RNA5


title: 103_P11_C09


title: 2D EC

description:
Library name: Sample 2
10X Genomics

source_name: 2D cell culture

value: 2D cell culture

value: GFP-HUVEC

value: endothelial cells

value: 2D monoculture


title: 2D CM

description:
Library name: Sample 1
10X Genomics

value: cardiomyocytes


title: ESC2i Mll2 KO Tamoxifen biol rep 2

description:
Library name: Sample 7
Column name in bfx754.mm10.e87.txt: RNA7


title: HH.P3

city: Chicago

first: Junzui

last: Li

state: IL

address: 303 E. Superior Street

department: OBGYN

institute: Northwestern University

description: Library name: HH.P3

data_processing:
Raw sequencing reads were quality-filtered and adaptor-trimmed using fastp. Clean reads were then aligned to the human reference genome (GRCh38/hg38) using HISAT2 with default parameters. Gene-level read counts were quantified using featureCounts (Subread package) based on the GENCODE human gene annotation. TPM values were calculated from raw gene counts after normalization for gene length and library size.
Assembly: hg38
Supplementary files format and content: Processed data files include a gene-level raw count matrix generated by featureCounts, with genes in rows and samples in columns.

growth_protocol: OVCAR5 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, and 1% L-GlutaMAX™ at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer's protocol.  RNA quantity and integrity were assessed using NanoDrop and Agilent Bioanalyzer.
RNA-seq libraries were prepared using an Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s protocol. Poly(A)+ mRNA was enriched, fragmented, and reverse-transcribed to cDNA, followed by end repair, A-tailing, adaptor ligation, and PCR amplification. Final libraries were quantified and assessed for quality before sequencing.

treatment_protocol: Stable METTL3-overexpressing OVCAR5 cell lines were generated via lentiviral transduction using METTL3-overexpression constructs. Following infection, cells were selected with puromycin until stable expression was established. Control cell lines were generated in parallel using empty-vector lentivirus. Cells were expanded under standard culture conditions and harvested for RNA extraction.

value: epithelial cancer cell line


title: ESC2i Bod1L WT biol rep 2

description:
Library name: Sample 4
Column name in bfx754.mm10.e87.txt: RNA4


title: 103_P11_C08


title: ESC2i Bod1L KO Tamoxifen biol rep 1

description:
Library name: Sample 1
Column name in bfx754.mm10.e87.txt: RNA1


title: ESC2i Bod1L KO Tamoxifen biol rep 2

description:
Library name: Sample 3
Column name in bfx754.mm10.e87.txt: RNA3


title: HH.P2

description: Library name: HH.P2


title: HH.P1

description: Library name: HH.P1


title: #4 KTC;Trp53fl/fl  (WES)

city: Stanford

first: Sofia

last: Ferreira

state: CA

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University School of Medicine

description: Library name: BF2154 (KPT)

library_source: genomic

data_processing:
We used 10X Genomics Long Ranger pipeline to map the reads to the mm10 reference mouse genome, resulting in BAM and BAI files. We ran the Genome Analysis Toolkit (GATK), CollectReadCounts algorithm on the BAM and BAI files and the S0276129.bed file (supplied by Agilent corresponding to the SureSelect XT2 exon capture kit) to obtain coverage for all samples. To alleviate the use of a panel of normals, coverages of each exon in each sample were first normalized sample-to-sample (normalization of sequencing depth), by dividing coverage values by the median values of coverages in each sample. In a second step of normalization, coverages were normalized exon-to-exon (normalization of exome capture kit affinity bias) by dividing coverage values by the median value for the given exome across all samples. On these double-normalized coverage values, the GATK ModelSegments and CallCopyRatioSegments algorithms were called, to identify segments of the genome with copy number variations (CNV).
Assembly: Reads were aligned to the GRCm38 mouse genome using HISAT2 (v 2.0.4; RRID:SCR_015530)

molecule: genomic DNA

source_name: Pancreatic Ductal Adenocarcinoma

growth_protocol: Unless indicated otherwise, mice were aged until morbidity.

extract_protocol:
Puregene Tissue Kit (QIAGEN; catalog no. 158667)
Libraries were prepared using the 10x Genomics Chromium Genome Library & Gel Bead Kit v2 for Exome Application (PN-1000017) in conjugation with the Agilent SureSelect XT Mouse All Exon Enrichment System (PN 5190-4641) for targeted exome enrichment.

treatment_protocol: At 8-10 weeks of age, mice were administered 5 mg tamoxifen dissolved in 2% ethanol/corn oil via oral gavage once per day for 3 consecutive days.

value: Pancreatic Ductal Adenocarcinoma

value: Acinar-derived Pancreatic Ductal Adenocarcinoma

value: KTC;Trp53fl/fl (K= KrasLSL-G12D; T=Rosa26LSL-tdTomato/LSL-tdTomato; C= Ptf1aCreER)


title: ESC2i Bod1L WT biol rep 1

description:
Library name: Sample 2
Column name in bfx754.mm10.e87.txt: RNA2

value: Naive Embryonic Stem Cells


title: 103_P11_C06


title: #3 KTC;Trp53fl/fl  (WES)

description: Library name: BF2117 (KPT)


title: 103_P11_C07


title: 103_P11_C05


title: ESC2i Setd1a KO Tamoxifen biol rep 1

description:
Library name: Sample 9
Column name in bfx754.mm10.e87.txt: RNA9

value: Setd1a KO

value: Media with LIF, PD0325901 and CT99021


title: #2 KTC;Trp53fl/fl  (WES)

description: Library name: BF1987 (KPT)


title: HH.MT3

description: Library name: HH.MT3


title: #1 KTC;Trp53fl/fl  (WES)

description: Library name: BF1905 (KPT)


title: #7 KrasLSL-G12D;Rosa26LSL-tdTomato/LSL-tdTomato;Ptf1aCreER (WES)

description: Library name: CS751 (KT)


title: HH.MT2

description: Library name: HH.MT2


title: 103_P11_C04


title: #6 KrasLSL-G12D;Rosa26LSL-tdTomato/LSL-tdTomato;Ptf1aCreER (WES)

description: Library name: BF3069 (KT)


title: #4 KrasLSL-G12D;Rosa26LSL-tdTomato/LSL-tdTomato;Ptf1aCreER (WES)

description: Library name: BF1221 (KT)


title: 103_P11_C03


title: #5 KrasLSL-G12D;Rosa26LSL-tdTomato/LSL-tdTomato;Ptf1aCreER (WES)

description: Library name: BF3063 (KT)


title: HH-SM4-3

description: Library name: HH-SM4-3

treatment_protocol: Stable cell lines were generated via lentiviral transduction and subsequent puromycin selection. Following antibiotic selection, successfully transduced cells were expanded under standard culture conditions and harvested for RNA extraction.


title: #3 KrasLSL-G12D;Rosa26LSL-tdTomato/LSL-tdTomato;Ptf1aCreER (WES)

description: Library name: BF972 (KT)


title: 103_P11_C02


title: HH-SM4-2

description: Library name: HH-SM4-2


title: Tsc_45 days_6

city: Albuquerque

first: Marybeth

last: Brooks

state: New Mexico

address: 915 Camino de Salud

department: DOIM - Nephrology

institute: University of New Mexico

description:
Library name: Tsc6
MS6_S12
Actual Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)

data_processing:
Clean reads were aligned to a mouse reference genome using Hisat2 v2.0.4. Gene.
Assembly: The gene expression levels were determined using fragments per kilobase of transcript per million mapped fragments (FPKM) by HTSeq v0.9.1.
Supplementary files format and content: xlsx

source_name: kidney

extract_protocol:
Total kidney RNA was isolated using a Tri-Reagent protocol. The isolated RNA samples were ethanol precipitated, dissolved in water, and subjected to quality control analysis using an Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA).
RNA samples were subjected to poly A selection, fragmented, and reverse-transcribed to generate complementary DNA libraries that were utilized for sequencing analysis. Libraries were sequenced using the HiSeqTM 2500 system (Illumina).

value: kidney

value: Tsc1f/f/Aqp2 Cre

tag: age

value: 45 days


title: #2 KrasLSL-G12D;Rosa26LSL-tdTomato/LSL-tdTomato;Ptf1aCreER (WES)

description: Library name: BF858 (KT)


title: #1 KrasLSL-G12D;Rosa26LSL-tdTomato/LSL-tdTomato;Ptf1aCreER (WES)

description: Library name: BF575 (KT)


title: 103_P11_C01

value: Melanoma cell line-derived tumor

value: HGF-tg C57BL6


title: 103_P11_B12

value: CD45-, CD31-, alive, nucleated cells


title: Tsc_45 days_4

description:
Library name: Tsc4
MS4_S10
Actual Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)


title: HH-SM2-3

description: Library name: HH-SM2-3


title: Tsc_45 days_5

description:
Library name: Tsc5
MS5_S11
Actual Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)


title: 103_P11_B10


title: HH.MT1

description: Library name: HH.MT1


title: WT_45 days_2

description:
Library name: WT2
MS2_S8
Actual Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)


title: TSC_28 days_8

description:
Library name: TSC8
Actual Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)

value: 28 days


title: WT_45 days_1

description:
Library name: WT1
MS1_S7
Actual Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)


title: HH-SM2-2

description: Library name: HH-SM2-2


title: 103_P11_B09


title: HH-SM2-1

description: Library name: HH-SM2-1


title: HH-SM4-1

description: Library name: HH-SM4-1


title: WT_28 days_4

description:
Library name: WT4
Actual Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)


title: TSC_28 days_5

description:
Library name: TSC5
Actual Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)


title: HH-NC-3

description: Library name: HH-NC-3


title: TSC_28 days_7

description:
Library name: TSC7
Actual Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)


title: WT_45 days_3

description:
Library name: WT3
MS3_S9
Actual Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)


title: 103_P11_B07

description: Expression_CountValue.tsv,Expression_FPKM.tsv,Expression_TPM.tsv,Mutations.tsv


title: 103_P11_B08


title: HH-NC-1

description: Library name: HH-NC-1


title: WT_28 days_3

description:
Library name: WT3
Actual Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)


title: WT_28 days_1

description:
Library name: WT1
Actual Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)


title: T12

description:
Library name: T12
Acutal Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)

data_processing:
Clean reads were aligned to a mouse reference genome using Hisat2 v2.0.4. Gene.
Assembly: The gene expression levels were determined using fragments per kilobase of transcript per million mapped fragments (FPKM) by HTSeq v0.9.1. The enrichment analysis of DET were performed using ShinyGO application (http://bioinformatics.sdstate.edu/go/, 02-19-2024).
Supplementary files format and content: xlsx

extract_protocol:
Total kidney RNA was isolated using a Tri-Reagent Protocol. The isolated RNA samples were ethanol precipitated, dissolved in water, and subjected to quality control analysis using an Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA).
RNA samples were subjected to poly A selection, fragmented, and reverse-transcribed to generate complementary DNA libraries that were utilized for sequencing analysis. Libraries were sequenced using the HiSeqTM 2500 system (Illumina).

value: Tsc1f/f/Aqp2 Cre/Foxi1 knockout


title: ILF3_KO_gene_10x_lane2

city: Cambridge

first: Mohamed

middle: A.

last: El-Brolosy

state: MA

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

description: Library name: Sample5

data_processing:
Following sequencing, reads were used as input to Cell Ranger v6.1.2 for alignment.
Assembly: GRCh38
Supplementary files format and content: tab separated value files, matrix files, h5 file and protocopacer calls per cells\

molecule: polyA RNA

source_name: cell line

extract_protocol:
Cells were prepared for single-cell RNA-sequencing by resuspension in 1X PBS with 0.04% BSA as detailed in the 10x Genomics Single Cell Protocols Cell Preparation Guide (10x Genomics, CG00053 Rev C). For the WT experiment, cells were then separated into droplet emulsions using the Chromium Controller (10x Genomics) with Chromium Single-Cell 3′ Gel Beads v3 (10x Genomics, PN-1000075) across 3 “lanes”/”GEM groups” following the 10x Genomics Chromium Single Cell 3ʹ Reagent Kits v3 User Guide with Feature Barcode technology for CRISPR Screening (CG000184 Rev C) with the goal of recovering ∼20,000 cells per GEM group.  For the ILF3 KO cells were cells were separated into droplet emulsions using the Chromium Controller (10x Genomics) with Chromium Single Cell 3’ HT Gel Bead Kit v3.1 (10x Genomics, PN-1000370) across 2 “lanes”/”GEM groups” following the Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 User Guide with Feature Barcode technology for CRISPR Screening (CG000421Rev D) with the goal of recovering ∼30,000 cells per GEM group before filtering.
For preparation of gene expression and sgRNA libraries, samples were processed according to 10x Genomics Chromium Single Cell 3ʹ Reagent Kits v3 or HT v3.1 User Guide with Feature Barcode technology for CRISPR Screening (CG000184 Rev C, CG000421Rev D). For sequencing, mRNA and sgRNA libraries were pooled to avoid index collisions at a 10:1 ratio.

value: cell line

value: myelogenous leukemia cell line

value: ILF3 KO


title: T11

description:
Library name: T11
Acutal Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)


title: ILF3_KO_gene_10x_lane1

description: Library name: Sample4


title: WT_28 days_2

description:
Library name: WT2
Actual Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)


title: T9

description:
Library name: T9
Acutal Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)


title: T10

description:
Library name: T10
Acutal Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)


title: WT4

description:
Library name: WT4
Acutal Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)


title: 103_P11_B04


title: ILF3_KO_gRNA_10x_lane2

description: Library name: Sample2

library_source: other

molecule: other


title: 103_P11_B03


title: WT1

description:
Library name: WT1
Acutal Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)


title: WT3

description:
Library name: WT3
Acutal Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)


title: 103_P11_B05


title: HH-NC-2

description: Library name: HH-NC-2

value: epithelial cancer cell line


title: ESC, beta KO, rep1

city: Jerusalem

first: Eran

last: Meshorer

address: Institute of Life Sciences, The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram

department: Department of Genetics

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Sequenced reads were aligned with STAR (v2.5.4b) using default parameters to the mouse genome and transcriptome from ENSEMBL (GRCm38.97)
Gene counts were obtained using featureCounts (Subread package v2.0.0) with default parameters
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts for each gene in every sample

growth_protocol: Mouse ESCs were cultured on MEF coated plates, in DMEM (Sigma) supplemented with 15% FBS (Biological Industries), L‐glutamine, 1X MEM non‐essential amino acids, Sodium Pyruvate, 1x Penstrep, 0.2 mM β-ME and LIF.

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Qiagen).
500ng of RNA was used to generate libraries with QuantSeq 3’ mRNASeq Kit (Lexogen) according to the manufacturer's instructions.

value: Embryonic Stem Cells

value: SET BKO

value: no dox


title: ESC, alpha KO, rep6

value: SET AKO


title: WT2

description:
Library name: WT2
Acutal Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)


title: 103_P11_A10


title: ESC, alpha KO, rep3


title: ILF3_KO_gRNA_10x_lane1

description: Library name: Sample1


title: 103_P11_B02


title: ESC, beta KO, rep4


title: SW620 cells,shDNM1-3

city: Shanghai

first: Rui

last: Chen

address: No. 128 Ruili Road, Minhang District

country: China

institute: The Fifth People's Hospital of Shanghai, Fudan University

description: Library name: sh1_3

data_processing:
CLC Workbench v.23.0
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: colon

growth_protocol: SW620 cells were cultured in high-glucose DMEM containing 10% fetal bovine serum under standard conditions (37°C, 5% CO2) in an incubator

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen) following manufacturer's insctucture..
RNA libraries were prepared using SMARTER mRNA-seq Library Prep kit following manufacturer's insctucture.

value: colon

value: human colon cancer cell

value: DNM1 Knockdown

tag: batch


title: SW620 cells,shControl-1

description: Library name: shCon_1

value: WT


title: SW620 cells,shControl-3

description: Library name: shCon_3


title: 103_P11_B01

value: Melanoma cell line-derived tumor


title: ESC, beta KO, rep3


title: 103_P11_A08

value: HGF-tg C57BL6


title: ESC, WT, rep4


title: 230922-RN01

city: Houston

first: Jennifer

last: Wang

state: TX

address: 1515 Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

description: Library name: Sample 109

data_processing:
Raw RNA sequencing reads of the samples were mapped to the hg19 reference genome using the STAR aligner.
RSEM was used to quantify aligned reads and produce raw counts of known transcripts
The raw count of transcripts in the samples were then converted to transcripts per million that normalize counts for library size and gene length.
Assembly: GRCh37
Supplementary files format and content: AllSamples_rawcount.txt (raw count data): tab-delimited text file
Supplementary files format and content: AllSamples_TPM.txt (Transcripts Per Million, TPM data): tab-delimited text file

source_name: Papillary Thyroid Carcinoma

extract_protocol:
RNA was extracted by Qiagen RNeasy Mini Kit (Cat. 74106) (Qiagen Inc.). The extracted RNA was treated with DNase I to get rid of nay genomic DNA residues. The treated RNA then was cleaned-up using the AMPure XP beads (Beckman Coulter Life Sciences) and eluted into 1x TE buffer. The purified RNA was quantified using Quant-iT™ RiboGreen™ RNA Assay Kit (ThermoFisher SCIENTIFIC) and the RNA quality was accessed using Agilent RNA 6000 Nano Kit and the 2100 Bioanalyzer Instrument (Agilent Technologies).
The fragmented cDNA was proceeded to library preparation using SureSelect XT Low Input Reagent Kit with indexes 1-96 (Cat: G9703A, Agilent Technologies) and automated on the Sciclone G3 NGSx Workstation (PerkinElmer, Inc.). This protocol consists of 3 enzymatic reactions for end repair, A-tailing and Adaptor ligation, followed by barcode insertion by PCR using Herculase II Fusion DNA Polymerase (8 to 14 cycles, based on input DNA quality and quantity). PCR primers were removed by using 1x volume of Agencourt AMPure PCR Purification kit (Agencourt Bioscience Corporation). The quality and quantity of the prepared libraries were evaluated using TapeStation 4200 and the DNA High Sensitivity kit (Agilent Technologies) to verify correct fragment size and to ensure complete removal of primer dimers.

value: Papillary Thyroid Carcinoma


title: ESC, WT, rep6


title: 103_P11_B11

value: CD45-, CD31-, alive, nucleated cells


title: ESC, beta KO, rep2


title: 103_P11_A12


title: SW620 cells,shDNM1-1

description: Library name: sh1_1


title: ESC, WT, rep1


title: ESC, alpha KO, rep5


title: TSC_28 days_6

description:
Library name: TSC6
Actual Model Used - Agilent 2100 Bioanalyzer with RNA 6000 Nano Kits (Agilent, USA)

value: kidney

value: Tsc1f/f/Aqp2 Cre

value: 28 days


title: ESC, alpha KO, rep2


title: 103_P11_B06


title: ESC, alpha KO, rep4


title: 103_P11_A11


title: 231353-RN01

description: Library name: Sample 106


title: ESC, alpha KO, rep1


title: 103_P11_A09


title: SW620 cells,shControl-2

description: Library name: shCon_2


title: SW620 cells,shDNM1-2

description: Library name: sh1_2


title: ESC, WT, rep5


title: adjacent uninvolved liver tissue 2

city: Birmingham

first: Amr

last: Elkholy

state: AL

address: 1824 6th Ave S, WTI 330A B

institute: University of Alabama at Birmingham

description: Library name: Control_2

data_processing:
Raw sequencing reads in FASTQ format were processed with Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adapter sequences and low-complexity regions.
Trimmed reads were mapped to the human reference genome (hg38) using HISAT.
Aligned tools were sorted with Samtools, and gene-level read counts were generated using HTSeq.
Assembly: hg38
Supplementary files format and content: txt File

source_name: adjacent uninvolved liver tissue

extract_protocol:
Both tumor and normal liver tissues were macro-dissected, and total RNA was extracted using the All Prep DNA/RNA FFPE Kit (Cat #80234, Qiagen, Germantown, MD) following the manufacturer’s protocol. The integrity and quantity of isolated RNA were evaluated using the Tape Station with High Sensitivity RNA Screen Tape (Cat #5067–5579, Agilent Technologies, Santa Clara, CA) and Qubit RNA assay kit (Cat #Q32855, Invitrogen, Thermo Fisher Scientific, Waltham, MA).
For RNA library preparation, we utilized the SureSelectXT Low Input library preparation and target enrichment kit (Cat #5190–9686, Agilent Technologies, Santa Clara, CA). Libraries were pooled in 12-plex format and sequenced to a read depth of 30 million reads per sample using single-end reads on the NextSeq 500/550 platform with the High Output reagent cartridge v2 (Cat #, 15057934, Illumina, San Diego, CA).

value: adjacent uninvolved liver tissue


title: 230940-RN01

description: Library name: Sample 105


title: 103_P11_A04


title: solid-tubulocystic variant of intrahepatic cholangiocarcinoma (ST-iCCA) with pseudoglandular (PG) growth pattern 1

description: Library name: Pseudoglandular_1


title: ESC, WT, rep3


title: 231357-RN01

description: Library name: Sample 108


title: ESC, WT, rep2


title: 103_P11_A07


title: 230939-RN01

description: Library name: Sample 104


title: 230938-RN01

description: Library name: Sample 103


title: 103_P11_A02


title: solid-tubulocystic variant of intrahepatic cholangiocarcinoma (ST-iCCA) with solid/pseudopapillary (PP) growth pattern 2

description: Library name: Pseudopapillary_2


title: 231354-RN01

description: Library name: Sample 107


title: solid-tubulocystic variant of intrahepatic cholangiocarcinoma (ST-iCCA) with solid/pseudopapillary (PP) growth pattern 1

description: Library name: Pseudopapillary_1


title: 103_P11_A06


title: FADU, normoxia, H4K5Ac

city: Taoyuang

first: Kou-Juey

last: Wu

state: Taiwan

address: No.15, Wenhua 1st Road, Gueishan Dist

department: Cancer Genome Research Center

country: Taiwan

institute: Chang Gung Memorial Hospital at Linkou

description: Library name: H4K5Ac_N

data_processing:
Sequencing reads were processed according to the procedure used in the 6mA-ChIP-exo-5.1 sequencing analysis. Quality control of all alignment files and the estimation of fragment sizes were performed using the SPP. For H3K4me1, broad peaks were identified using MACS2 with the parameters ‘-f BED -g hs –nomode –broad –keep-dup all –p 0.01’. For H3K4me3 and H3K27Ac, narrow peaks were identified using MACS2 with the parameters ‘-f BED -g hs –nomode –keep-dup all –p 0.01’. Differential histone modification occupancy analysis was performed using the SICER with the comparison of hypoxia versus normoxia for each histone mark.
Assembly: hg38
Supplementary files format and content: narrowPeak

source_name: FADU

growth_protocol: FaDu cells, a head and neck cancer cell line, were purchased from the Bioresource Collection and Research Center (BCRC, Hsinchu, Taiwan). The cell line was cultured in Dulbecco’s modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1 mM sodium pyruvate and 1 × Antibiotic–Antimycotic (Gibco), under the conditions of 5% CO2 at 37°C. The absence of mycoplasma was tested by the Mycoplasma PCR Detection Kit (abm) before the experiments. Knockdown of METTL4 was achieved using a previously established method with lentivirus infection. For hypoxic conditions, cells were incubated in an environment of 1% O2, 5% CO2 and 94% N2 at 37°C for a period of 18 h.

extract_protocol:
ChIP DNA was purified using DNA concentrator-5 (Zymo).
Library construction was performed using KAPA HyperPrep Kits. The libraries were sequenced on the Illumina Nextseq 550 platform to generate 75 bp single-end reads.

value: FADU


title: RNA-seq of HIF-2 Knockout Clone B, TIFM/Hypoxia (R26) replicate 3

city: Farmington

first: Yasir

last: Suhail

state: Connecticut

address: 263 Farmington Avenue

department: BME

institute: UCHC

description: Library name: R26 (HIF2)

data_processing:
Aligned wth HISAT2 using prebuilt index, gene counts by featureCounts
Assembly: Grch38
Supplementary files format and content: Raw counts TSV

extract_protocol:
Standard total RNA extraction using established laboratory protocols.
Standard RNA-seq library preparation using established commercial kits and manufacturer protocols.

value: Carcinoma

value: HIF2aKD, Clone B


title: RNA-seq of Control, Hypoxia/TIFM Media (R3E) replicate 3

description: Library name: R3E

value: Cntrl


title: 103_P11_A05


title: solid-tubulocystic variant of intrahepatic cholangiocarcinoma (ST-iCCA) with pseudoglandular (PG) growth pattern 2

description: Library name: Pseudoglandular_2


title: 103_P09_H11


title: adjacent uninvolved liver tissue 1

description: Library name: Control_1


title: 103_P11_A03


title: 230934-RN01

description: Library name: Sample 100


title: RNA-seq of HIF-2 Knockout Clone A, TIFM/Hypoxia (R23) replicate 3

description: Library name: R23 (HIF2)

value: HIF2aKD, Clone A


title: 103_P09_H10


title: FADU, hypoxia, H4K5Ac

description: Library name: H4K5Ac_H


title: 230936-RN01

description: Library name: Sample 102


title: RNA-seq of HIF-2 Knockout Clone A, TIFM/Hypoxia (R22) replicate 2

description: Library name: R22 (HIF2)


title: RNA-seq of Control, Hypoxia/TIFM Media (R2E) replicate 2

description: Library name: R2E


title: RNA-seq of Control, Hypoxia/TIFM Media (R1E) replicate 1

description: Library name: R1E


title: 230935-RN01

description: Library name: Sample 101


title: 230932-RN01

description: Library name: Sample 98


title: 103_P09_H12


title: RNA-seq of HIF-2 Knockout Clone B, TIFM/Hypoxia (R24) replicate 1

description: Library name: R24 (HIF2)


title: 103_P09_H09


title: 103_P11_A01


title: RNA-seq of HIF-2 Knockout Clone B, TIFM/Hypoxia (R25) replicate 2

description: Library name: R25 (HIF2)


title: RNA-seq of Control, Normoxia/Regular Media (N2E) replicate 2

description: Library name: N2E

value: Normoxia


title: 103_P09_H07


title: RNA-seq of HIF-2 Knockout Clone A, TIFM/Hypoxia (R21) replicate 1

description: Library name: R21 (HIF2)


title: 230933-RN01

description: Library name: Sample 99


title: 230930-RN01

description: Library name: Sample 96


title: RNA-seq of HIF-1 Knockout, Hypoxia/TIFM (R11) replicate 1

description: Library name: R11 (HIF1)


title: 103_P09_H08


title: RNA-seq of HIF-1 Knockout, Hypoxia/TIFM (R12) replicate 2

description: Library name: R12 (HIF1)


title: RNA-seq of Control, Hypoxia/Regular Media (H2E) replicate 2

description: Library name: H2E

value: Hypoxia


title: 230931-RN01

description: Library name: Sample 97


title: RNA-seq of HIF-1 Knockout, Hypoxia/TIFM (R13) replicate 3

description: Library name: R13 (HIF1)


title: RNA-seq of HIF-2 Knockout Clone B, Normoxia/Regular  (N26) replicate 3

description: Library name: N26 (HIF2)


title: RNA-seq of HIF-2 Knockout Clone B, Normoxia/Regular  (N24) replicate 1

description: Library name: N24 (HIF2)


title: 230927-RN01

description: Library name: Sample 93


title: 103_P09_H06


title: RNA-seq of Control, Normoxia/Regular Media (N3E) replicate 3

description: Library name: N3E


title: RNA-seq of Control, Hypoxia/Regular Media (H3E) replicate 3

description: Library name: H3E


title: RNA-seq of Control, Hypoxia/Regular Media (H1E) replicate 1

description: Library name: H1E


title: 103_P09_H04


title: 230929-RN01

description: Library name: Sample 95


title: RNA-seq of Control, Normoxia/Regular Media (N1E) replicate 1

description: Library name: N1E


title: 230928-RN01

description: Library name: Sample 94


title: 103_P09_H02


title: RNA-seq of HIF-2 Knockout Clone A, Normoxia/Regular  (N22) replicate 2

description: Library name: N22 (HIF2)


title: RNA-seq of HIF-1 Knockout, Normoxia/Regular Media (N12) replicate 2

description: Library name: N12


title: 103_P09_H05


title: 103_P09_H01


title: RNA-seq of HIF-1 Knockout, Normoxia/Regular Media (N11) replicate 1

description: Library name: N11


title: RNA-seq of HIF-2 Knockout Clone B, Hypoxia/Regular  (H26) replicate 3

description: Library name: H26


title: RNA-seq of HIF-2 Knockout Clone B, Hypoxia/Regular  (H25) replicate 2

description: Library name: H25


title: 230926-RN01

description: Library name: Sample 92


title: RNA-seq of HIF-2 Knockout Clone B, Normoxia/Regular  (N25) replicate 2

description: Library name: N25 (HIF2)


title: RNA-seq of HIF-1 Knockout, Normoxia/Regular Media (N13) replicate 3

description: Library name: N13


title: RNA-seq of HIF-2 Knockout Clone A, Hypoxia/Regular  (H23) replicate 3

description: Library name: H23


title: 103_P09_G12


title: 103_P09_H03


title: 230925-RN01

description: Library name: Sample 91


title: RNA-seq of HIF-2 Knockout Clone A, Hypoxia/Regular  (H21) replicate 1

description: Library name: H21


title: RNA-seq of HIF-2 Knockout Clone A, Normoxia/Regular  (N21) replicate 1

description: Library name: N21 (HIF2)


title: RNA-seq of HIF-2 Knockout Clone A, Normoxia/Regular  (N23) replicate 3

description: Library name: N23 (HIF2)


title: 103_P09_G10


title: 230924-RN01

description: Library name: Sample 90


title: 230923-RN01

description: Library name: Sample 89


title: 103_P09_G08


title: Bulk RNA-seq, gRNA7, Cas9, Day25, R2

city: Barcelona

first: Yolanda

last: Andres Lopez

address: C/ Baldiri Reixac, 4-8

country: Spain

institute: Institute of Molecular Biology of Barcelona

data_processing:
Raw data was processed to extract nucleotide sequences and corresponding quality scores.
The raw reads containing the flanking regions of the barcode (U6 promoter and spacer). Barcodes with mean Illumina Phred scores below 28 were discarded. For the remaining reads, alignment was performed using the pairwiseAlignment function from the Biostrings R package. Alignment scores were normalized across all conditions, and aligned sequences were analyzed to compute nucleotide frequencies per position.
Assembly: mm10
Supplementary files format and content: The tab-delimited matrix with processed data per samples

source_name: mouse embryonic stem cells

growth_protocol: The cells were cultured at 37°C in a 5% CO2 atmosphere on gelatin-coated culture plates. They were passaged every other day using trypsin-EDTA.

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen, 74004) for bulk barcoding at various time points after cell sorting.
To amplify the gRNA loci, reverse transcription was performed with 1 µl of a primer and 500 ng of RNA. cDNA was amplified in a 20 µl reaction using KAPA HiFi HotStart ReadyMix (KAPA Biosystems, KK2502) with specific primers. PCR products were purified using AMPure XP Beads and sequenced on a single end Illumina MiSeq run with 58 cycles and an 8-cycle index.

value: mouse embryonic stem cells

tag: time

value: Day 25


title: RNA-seq of HIF-2 Knockout Clone B, Hypoxia/Regular  (H24) replicate 1

description: Library name: H24


title: 230918-RN01

description: Library name: Sample 85


title: 230919-RN01

description: Library name: Sample 86


title: 103_P09_G07

value: Melanoma cell line-derived tumor


title: RNA-seq of HIF-2 Knockout Clone A, Hypoxia/Regular  (H22) replicate 2

description: Library name: H22


title: 103_P09_G11

value: HGF-tg C57BL6


title: 230916-RN01

description: Library name: Sample 84

value: Papillary Thyroid Carcinoma


title: 230920-RN01

description: Library name: Sample 87


title: RNA-seq of HIF-1 Knockout, Hypoxia/Regular  (H13) replicate 3

description: Library name: H13


title: Bulk RNA-seq, gRNA7, Cas9, Day10, R2

value: Day 10


title: RNA-seq of HIF-1 Knockout, Hypoxia/Regular  (H12) replicate 2

description: Library name: H12


title: RNA-seq of HIF-1 Knockout, Hypoxia/Regular  (H11) replicate 1

description: Library name: H11


title: 103_P09_G09

value: CD45-, CD31-, alive, nucleated cells


title: 230914-RN01

description: Library name: Sample 82


title: 103_P09_G05


title: Bulk RNA-seq, gRNA7, Cas9, Day8, R2

value: Day 8


title: 230913-RN01

description: Library name: Sample 81


title: Bulk RNA-seq, gRNA7, Cas9, Day18, R2

value: Day 18


title: 103_P09_G04


title: Bulk RNA-seq, gRNA7, Cas9, Day10, R2.2


title: 230921-RN01

description: Library name: Sample 88


title: Bulk RNA-seq, gRNA7, Cas9, Day4, R2.2

value: Day 4


title: 103_P09_G03


title: 230911-RN01

description: Library name: Sample 79


title: 103_P09_G06


title: Bulk RNA-seq, gRNA7, Cas9, Day4, R1


title: Bulk RNA-seq, gRNA6, Cas9, Day25, R2


title: Bulk RNA-seq, gRNA7, Cas9, Day18, R1


title: 230915-RN01

description: Library name: Sample 83


title: Bulk RNA-seq, gRNA7, Cas9, Day4, R2.3


title: Bulk RNA-seq, gRNA7, Cas9, Day8, R1


title: 230909-RN01

description: Library name: Sample 77


title: 103_P09_G02


title: 230912-RN01

description: Library name: Sample 80


title: Bulk RNA-seq, gRNA6, Cas9, Day4, R1


title: Bulk RNA-seq, gRNA6, Cas9, Day32, R2

value: Day 32


title: Bulk RNA-seq, gRNA6, Cas9, Day18, R2


title: Bulk RNA-seq, gRNA7, Cas9, Day4, R2


title: 103_P09_G01


title: 230910-RN01

description: Library name: Sample 78


title: Bulk RNA-seq, gRNA7, Cas9, Day0, R1

value: Day 0


title: Bulk RNA-seq, gRNA6, Cas9, Day8, R1


title: 103_P09_F09


title: 103_P09_F12


title: 103_P09_F11


title: 230908-RN01

description: Library name: Sample 76


title: Bulk RNA-seq, gRNA6, Cas9, Day10, R1


title: Bulk RNA-seq, gRNA5, Cas9, Day25, R2


title: 230905-RN01

description: Library name: Sample 73


title: Bulk RNA-seq, gRNA6, Cas9, Day0, R1


title: Bulk RNA-seq, gRNA5, Cas9, Day18, R1


title: 103_P09_F10


title: Bulk RNA-seq, gRNA6, Cas9, Day4, R2


title: Bulk RNA-seq, gRNA6, Cas9, Day2, R2

value: Day 2


title: 230907-RN01

description: Library name: Sample 75


title: Bulk RNA-seq, gRNA6, Cas9, Day18, R1


title: Bulk RNA-seq, gRNA5, Cas9, Day32, R2


title: 230906-RN01

description: Library name: Sample 74


title: Bulk RNA-seq, gRNA5, Cas9, Day18, R2


title: 103_P09_F08


title: Bulk RNA-seq, gRNA5, Cas9, Day10, R1


title: Bulk RNA-seq, gRNA5, Cas9, Day4, R2


title: 230902-RN01

description: Library name: Sample 70


title: 230901-RN01

description: Library name: Sample 69


title: Bulk RNA-seq, gRNA5, Cas9, Day2, R1


title: 103_P09_F04


title: Bulk RNA-seq, gRNA5, Cas9, Day2, R2


title: Bulk RNA-seq, gRNA5, Cas9, Day10, R2


title: 103_P09_F07


title: 230904-RN01

description: Library name: Sample 72


title: 230903-RN01

description: Library name: Sample 71


title: 103_P09_F06


title: 103_P09_F02


title: Bulk RNA-seq, gRNA5, Cas9, Day8, R1


title: Bulk RNA-seq, gRNA5, Cas9, Day0, R1


title: 103_P09_F03


title: Bulk RNA-seq, gRNA5, Cas9, Day4, R1.2


title: 103_P09_F05


title: 230900-RN01

description: Library name: Sample 68


title: Bulk RNA-seq, gRNA5, Cas9, Day4, R1


title: 103_P09_F01


title: Bulk RNA-seq, gRNA4, Cas9, Day10, R1


title: Bulk RNA-seq, gRNA4, Cas9, Day18, R2


title: Bulk RNA-seq, gRNA4, Cas9, Day32, R2


title: Bulk RNA-seq, gRNA4, Cas9, Day10, R2


title: 230897-RN01

description: Library name: Sample 66


title: 103_P09_E12


title: Bulk RNA-seq, gRNA4, Cas9, Day4, R1.2


title: 230898-RN01

description: Library name: Sample 67


title: 230895-RN01

description: Library name: Sample 64


title: Bulk RNA-seq, gRNA4, Cas9, Day4, R1


title: Bulk RNA-seq, gRNA4, Cas9, Day4, R2


title: 103_P09_E11


title: 230894-RN01

description: Library name: Sample 63


title: 103_P09_E10


title: 103_P09_E09


title: Bulk RNA-seq, gRNA4, Cas9, Day8, R1


title: 230893-RN01

description: Library name: Sample 62


title: 230896-RN01

description: Library name: Sample 65


title: Bulk RNA-seq, gRNA4, Cas9, Day0, R1


title: Bulk RNA-seq, gRNA4, Cas9, Day2, R1


title: Bulk RNA-seq, gRNA3, Cas9, Day32, R2


title: Bulk RNA-seq, gRNA4, Cas9, Day25, R2


title: Bulk RNA-seq, gRNA3, Cas9, Day18, R2


title: Bulk RNA-seq, gRNA3, Cas9, Day25, R2


title: 230892-RN01

description: Library name: Sample 61


title: Bulk RNA-seq, gRNA4, Cas9, Day2, R2


title: 103_P09_E07


title: Bulk RNA-seq, gRNA3, Cas9, Day18, R1


title: 103_P09_E08


title: 103_P09_E06


title: Bulk RNA-seq, gRNA3, Cas9, Day10, R1


title: Bulk RNA-seq, gRNA3, Cas9, Day8, R1


title: 103_P09_E05


title: Bulk RNA-seq, gRNA3, Cas9, Day10, R2


title: 230889-RN01

description: Library name: Sample 58


title: 230891-RN01

description: Library name: Sample 60


title: 230890-RN01

description: Library name: Sample 59


title: 230888-RN01

description: Library name: Sample 57


title: 103_P09_E03


title: Bulk RNA-seq, gRNA3, Cas9, Day4, R1.2


title: Bulk RNA-seq, gRNA3, Cas9, Day4, R1


title: 103_P09_E04


title: Bulk RNA-seq, gRNA3, Cas9, Day2, R2

value: Day 102


title: 103_P09_E02


title: Bulk RNA-seq, gRNA3, Cas9, Day0, R1

value: Day 100


title: Bulk RNA-seq, gRNA3, Cas9, Day2, R1

value: Day 101


title: 230887-RN01

description: Library name: Sample 56


title: Bulk RNA-seq, gRNA3, Cas9, Day4, R2


title: 230885-RN01

description: Library name: Sample 54


title: Bulk RNA-seq, gRNA2, Cas9, Day25, R2

value: Day 98


title: 230886-RN01

description: Library name: Sample 55


title: Bulk RNA-seq, gRNA2, Cas9, Day18, R2

value: mouse embryonic stem cells


title: Bulk RNA-seq, gRNA2, Cas9, Day18, R1


title: 103_P09_E01


title: 103_P09_D12


title: Bulk RNA-seq, gRNA2, Cas9, Day32, R2

value: Day 99


title: Bulk RNA-seq, gRNA2, Cas9, Day10, R2

value: Day 95


title: 230884-RN01

description: Library name: Sample 53


title: 103_P09_D11

value: Melanoma cell line-derived tumor

value: HGF-tg C57BL6


title: Bulk RNA-seq, gRNA2, Cas9, Day4, R1


title: 230883-RN01

description: Library name: Sample 52

value: Papillary Thyroid Carcinoma


title: Bulk RNA-seq, gRNA2, Cas9, Day8, R1

value: Day 94


title: Bulk RNA-seq, gRNA2, Cas9, Day4, R1.2


title: 230882-RN01

description: Library name: Sample 51


title: 103_P09_D10

value: CD45-, CD31-, alive, nucleated cells


title: Bulk RNA-seq, gRNA2, Cas9, Day4, R2


title: Bulk RNA-seq, gRNA2, Cas9, Day2, R2


title: 103_P09_D09


title: 103_P09_D08


title: Bulk RNA-seq, gRNA1, Cas9, Day32, R2


title: Bulk RNA-seq, gRNA2, Cas9, Day0, R1


title: 230881-RN01

description: Library name: Sample 50


title: Bulk RNA-seq, gRNA2, Cas9, Day2, R1


title: Bulk RNA-seq, gRNA1, Cas9, Day25, R2

value: Day 25


title: 230880-RN01

description: Library name: Sample 49


title: Bulk RNA-seq, gRNA1, Cas9, Day18, R1

value: Day 18


title: Bulk RNA-seq, gRNA1, Cas9, Day18, R2


title: 103_P09_D07


title: 230879-RN01

description: Library name: Sample 48


title: 103_P09_D06


title: 230878-RN01

description: Library name: Sample 47


title: Bulk RNA-seq, gRNA1, Cas9, Day8, R1

value: Day 8


title: Bulk RNA-seq, gRNA1, Cas9, Day10, R2

value: Day 10


title: 230877-RN01

description: Library name: Sample 46


title: Bulk RNA-seq, gRNA1, Cas9, Day4, R1.2

value: Day 4


title: 103_P09_D05


title: 103_P09_D04


title: Bulk RNA-seq, gRNA1, Cas9, Day2, R2

value: Day 2


title: Bulk RNA-seq, gRNA1, Cas9, Day2, R1


title: Bulk RNA-seq, gRNA1, Cas9, Day4, R1


title: Bulk RNA-seq, gRNA1, Cas9, Day0, R1

value: Day 0


title: 230876-RN01

description: Library name: Sample 45


title: Bulk RNA-seq, gRNA1, Cas9, Day4, R2


title: Bulk RNA-seq, gRNA7, BE3, Day32, R2

value: Day 32


title: Bulk RNA-seq, gRNA7, BE3, Day25, R2


title: 230875-RN01

description: Library name: Sample 44


title: 230873-RN01

description: Library name: Sample 42


title: 103_P09_D01


title: Bulk RNA-seq, gRNA7, BE3, Day18, R1


title: 103_P09_D03


title: 103_P09_C12


title: Bulk RNA-seq, gRNA7, BE3, Day10, R1


title: Bulk RNA-seq, gRNA7, BE3, Day4, R1.2


title: 230874-RN01

description: Library name: Sample 43


title: 230872-RN01

description: Library name: Sample 41


title: 103_P09_D02


title: Bulk RNA-seq, gRNA7, BE3, Day4, R1


title: 103_P09_C10


title: 230871-RN01

description: Library name: Sample 40


title: Bulk RNA-seq, gRNA7, BE3, Day0, R1


title: Bulk RNA-seq, gRNA6, BE3, Day32, R2


title: Bulk RNA-seq, gRNA7, BE3, Day2, R1


title: Bulk RNA-seq, gRNA7, BE3, Day10, R1.2


title: 230870-RN01

description: Library name: Sample 39


title: 230869-RN01

description: Library name: Sample 38


title: Bulk RNA-seq, gRNA6, BE3, Day25, R2


title: 103_P09_C11


title: Bulk RNA-seq, gRNA6, BE3, Day18, R1


title: 103_P09_C09


title: 103_P09_C08


title: Bulk RNA-seq, gRNA6, BE3, Day10, R2


title: Bulk RNA-seq, gRNA6, BE3, Day8, R1


title: 103_P09_C07


title: 103_P09_C06


title: Bulk RNA-seq, gRNA6, BE3, Day4, R2


title: 230867-RN01

description: Library name: Sample 36


title: Bulk RNA-seq, gRNA6, BE3, Day4, R1.2


title: 230866-RN01

description: Library name: Sample 35


title: Bulk RNA-seq, gRNA6, BE3, Day4, R1


title: 103_P09_C05


title: 103_P09_C04


title: Bulk RNA-seq, gRNA6, BE3, Day2, R1


title: Bulk RNA-seq, gRNA6, BE3, Day2, R2


title: 230865-RN01

description: Library name: Sample 34


title: 230864-RN01

description: Library name: Sample 33


title: Bulk RNA-seq, gRNA5, BE3, Day32, R2


title: 230868-RN01

description: Library name: Sample 37


title: Bulk RNA-seq, gRNA5, BE3, Day18, R1


title: Bulk RNA-seq, gRNA6, BE3, Day0, R1


title: 103_P09_C03


title: 230862-RN01

description: Library name: Sample 32


title: 103_P09_C02


title: Bulk RNA-seq, gRNA5, BE3, Day25, R2


title: Bulk RNA-seq, gRNA5, BE3, Day10, R2


title: Bulk RNA-seq, gRNA5, BE3, Day8, R1


title: 103_P09_C01


title: 0.5hr Glu_rep2

city: Taipei

first: Yi-Jie

last: Hung

address: 128 Section 2, Academia Road, Nankang

department: IPMB

institute: Academia Sinica

description:
Library name: Sample 4
Arabidopsis thaliana Col-0 seedlings treated with glutamate for 0.5 hr

data_processing:
Low quality reads, which are shorter than 35 base pairs or have an error probability greater than 0.05, were filtered out.
Mapping reads to the Arabidopsis reference genome TAIR10 by using BLAT method.
R1 BAM file of each sample under SAMtools.
For each sample, pick up R1 BAM file for reads per kilo-base-pair gene model per million mapped reads (RPKM) computation.
Assembly: TMM normalization is applied to normalize all RPKM files.
Supplementary files format and content: TAIR 10
Supplementary files format and content: tab-delimited text file include normalized RPKM values for each sample

organism: Arabidopsis thaliana

source_name: 14-day-old seedlings

growth_protocol: Arabidopsis seeds were surface sterilized and grown on a hydroponic solution box containing 1/2 MS-modified basal salt mixture without N (M531, PhytoTechnology Laboratories) adjusted to pH 5.7 with 1 N KOH. The box was kept at 4℃ for 2 days and then transferred to a growth chamber on a 16-h-light/8-h-dark cycle at 22°C for 14 days.

extract_protocol:
Total RNA was extracted using Trizol reagent. One mg total RNA was used for the construction of sequencing libraries using the Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Arabidopsis were be transferred to treatment which containing 1/2 MS-modified basal salt mixture without N (M531, PhytoTechnology Laboratories) plus 2.5 mM Glu, adjusted to pH 5.7 with 1 N KOH.

value: 14-day-old seedlings

tag: ecotype


title: 0.5hr Glu_rep1

description:
Library name: Sample 3
Arabidopsis thaliana Col-0 seedlings treated with glutamate for 0.5 hr


title: Bulk RNA-seq, gRNA5, BE3, Day4, R1.2

value: mouse embryonic stem cells


title: 103_P09_B12


title: 230861-RN01

description: Library name: Sample 31


title: 230859-RN01

description: Library name: Sample 29


title: 230860-RN01

description: Library name: Sample 30


title: Bulk RNA-seq, gRNA5, BE3, Day4, R2


title: Bulk RNA-seq, gRNA5, BE3, Day4, R1


title: 230858-RN01

description: Library name: Sample 28


title: 0hr Glu_rep2

description:
Library name: Sample 2
Arabidopsis thaliana Col-0 seedlings treated with glutamate for 0 hr


title: Bulk RNA-seq, gRNA5, BE3, Day2, R2


title: 103_P09_B10


title: 103_P09_B11


title: 230857-RN01

description: Library name: Sample 27


title: Bulk RNA-seq, gRNA5, BE3, Day2, R1


title: 103_P09_B09


title: 230856-RN01

description: Library name: Sample 26


title: 230855-RN01

description: Library name: Sample 25


title: Sample 15, Ty, without lesions

city: Derio

first: Marta

last: Alonso-Hearn

state: Bizkaia

address: Berreaga 1

department: Animal Health

institute: NEIKER

description:
Library name: Sample 15, JE
JE15

data_processing:
Raw reads were filtered and trimmed by their Phred quality score >30, length (>100 bp), and percentage of ambiguous bases (<10%), and aligned to the Bos taurus reference genome (ARS_UCD2.0) using the Spliced Transcripts Alignment to a Reference aligner (STAR 2.7.0a). The resulting aligned reads were used to generate a table of counts for each gene using the FeatureCounts function from the R library Rsubread 1.32.4. Gene counts were then normalized with the mean-of-ratios method included in the DESeq2 1.22.2 software. Differential expression analysis of mRNAs for the comparison of cows with multifocal lesions versus controls was performed with DESeq2.
Assembly: ARS-UCD2.0.114
Supplementary files format and content: txt containing the FPKMs of each gene for each sample, obtained with DESeq2 from the gene counts. First column is gene Ensembl ID. Each column after that is sample ID as indicated in the "description" field

organism: Bos taurus

source_name: Jejunum

extract_protocol:
RNA was extracted from PB, JE, and JELN of the 15 cows included in the study. PB samples were collected from the coccygeal vein of cows using PAXgene Blood RNA tubes (2.5 ml) (Qiagen, Hilden, Germany). Total RNA was extracted with the PAXgene blood RNA kit according to manufacturer’s instructions (Qiagen, Hilden, Germany). For RNA isolation from gut samples, 150–200 mg of JE and JELN were harvested and immediately submerged in 2 ml of RNA later (Sigma, St. Louis, MO). Purification of tissue RNA was performed using the RNeasy Mini Kit according to the manufacturer’s instructions (Qiagen, Hilden, Germany). Residual DNA was removed by digestion with RNase-free DNase I Amplification Grade (Invitrogen, Spain).
Each RNA library was prepared with approximately 250 ng of RNA using the Illumina NEBNext® Ultra Directional RNA library preparation kit (Illumina, San Diego, CA, US). The RNA-Seq libraries’ quality was assessed on the Agilent Bioanalizer using a highly sensitive DNA chip to confirm that the insert size was between 188-274 bp for all individual libraries. All RNA-Seq libraries were quantified using a Qubit® Fluorometer and doubled stranded DNA high Sensitivity Assay Kit (Invitrogen, Spain). Libraries were sequenced by single-end sequencing in 1x100 format on the Illumina NextSeq sequencer at the Genomic Unit of the Scientific Park of Madrid, Spain.

value: Jejunum

tag: sample group

value: without lesions


title: Sample 14, Ty, without lesions

description:
Library name: Sample 14, JE
JE14


title: 103_P09_B08

value: Melanoma cell line-derived tumor


title: 0hr Glu_rep1

description:
Library name: Sample 1
Arabidopsis thaliana Col-0 seedlings treated with glutamate for 0 hr


title: Bulk RNA-seq, gRNA5, BE3, Day0, R1


title: Sample 13, Ty, without lesions

description:
Library name: Sample 13, JE
JE13


title: 230854-RN01

description: Library name: Sample 24


title: Bulk RNA-seq, gRNA4, BE3, Day32, R2


title: 103_P09_B07

description: Expression_CountValue.tsv,Expression_FPKM.tsv,Expression_TPM.tsv,Mutations.tsv

value: HGF-tg C57BL6


title: Bulk RNA-seq, gRNA4, BE3, Day25, R2


title: Sample 11, Ty, with multifocal lesions

description:
Library name: Sample 11, JE
JE11

value: with multifocal lesions


title: 230852-RN01

description: Library name: Sample 22

value: Papillary Thyroid Carcinoma


title: 103_P09_B05

value: CD45-, CD31-, alive, nucleated cells


title: Sample 10, Ty, with multifocal lesions

description:
Library name: Sample 10, JE
JE10


title: 230853-RN01

description: Library name: Sample 23


title: Bulk RNA-seq, gRNA4, BE3, Day18, R2


title: 103_P09_B04


title: 103_P09_B06


title: 230851-RN01

description: Library name: Sample 21


title: Bulk RNA-seq, gRNA4, BE3, Day10, R1


title: Sample 9, Ty, with multifocal lesions

description:
Library name: Sample 9, JE
JE9


title: 103_P09_B03


title: Bulk RNA-seq, gRNA4, BE3, Day18, R1


title: Sample 12, Ty, without lesions

description:
Library name: Sample 12, JE
JE12


title: 103_P09_B02


title: 230849-RN01

description: Library name: Sample 20


title: Sample 8, Ty, with multifocal lesions

description:
Library name: Sample 8, JE
JE8


title: Bulk RNA-seq, gRNA4, BE3, Day10, R2


title: 230848-RN01

description: Library name: Sample 19


title: Sample 6 Ty, with multifocal lesions

description:
Library name: Sample 6 JE
JE6


title: Bulk RNA-seq, gRNA4, BE3, Day8, R1


title: 230847-RN01

description: Library name: Sample 18


title: Bulk RNA-seq, gRNA4, BE3, Day4, R1.2


title: 103_P09_B01


title: 103_P09_A12


title: Sample 5, Ty, with multifocal lesions

description:
Library name: Sample 5, JE
JE5


title: Sample 4, Ty, with multifocal lesions

description:
Library name: Sample 4, JE
JE4


title: Sample 2, Ty, with multifocal lesions

description:
Library name: Sample 2, JE
JE2


title: Bulk RNA-seq, gRNA4, BE3, Day4, R2


title: 230845-RN01

description: Library name: Sample 16


title: 230844-RN01

description: Library name: Sample 15


title: Sample 1, Ty, with multifocal lesions

description:
Library name: Sample 1, JE
JE1


title: Bulk RNA-seq, gRNA4, BE3, Day4, R1


title: Bulk RNA-seq, gRNA4, BE3, Day2, R2


title: 103_P09_A11


title: 103_P09_A09


title: Bulk RNA-seq, gRNA4, BE3, Day2, R1


title: 230846-RN01

description: Library name: Sample 17


title: Sample 13, Tg, without lesions

description:
Library name: Sample 13, JELN
JELN13

source_name: Jejunal lymph node

value: Jejunal lymph node


title: 103_P09_A10


title: 230842-RN01

description: Library name: Sample 13


title: Bulk RNA-seq, gRNA3, BE3, Day32, R2


title: Sample 14, Tg, without lesions

description:
Library name: Sample 14, JELN
JELN14


title: 103_P09_A07


title: 230840-RN01

description: Library name: Sample 11


title: Sample 12, Tg, without lesions

description:
Library name: Sample 12, JELN
JELN12


title: 103_P09_A05


title: 103_P09_A06


title: 230839-RN01

description: Library name: Sample 10


title: 230843-RN01

description: Library name: Sample 14


title: 230841-RN01

description: Library name: Sample 12


title: Sample 10, Tg, with multifocal lesions

description:
Library name: Sample 10, JELN
JELN10


title: 103_P09_A08


title: Bulk RNA-seq, gRNA3, BE3, Day25, R2

value: Day 25


title: 103_P09_A04


title: Bulk RNA-seq, gRNA4, BE3, Day0, R1


title: Sample 9, Tg, with multifocal lesions

description:
Library name: Sample 9, JELN
JELN9


title: Bulk RNA-seq, gRNA3, BE3, Day10, R2


title: Sample 11, Tg, with multifocal lesions

description:
Library name: Sample 11, JELN
JELN11


title: 103_P09_A03


title: 230838-RN01

description: Library name: Sample 9


title: 230837-RN01

description: Library name: Sample 8


title: Sample 7, Tg, with multifocal lesions

description:
Library name: Sample 7, JELN
JELN7


title: 103_P09_A02


title: Bulk RNA-seq, gRNA3, BE3, Day8, R1

value: Day 27


title: Bulk RNA-seq, gRNA3, BE3, Day4, R1


title: 230835-RN01

description: Library name: Sample 6


title: Bulk RNA-seq, gRNA3, BE3, Day18, R1

value: Day 18


title: 103_P09_A01


title: 230836-RN01

description: Library name: Sample 7


title: 103_P05_H12


title: Sample 6 Tg, with multifocal lesions

description:
Library name: Sample 6, JELN
JELN6


title: 230834-RN01

description: Library name: Sample 5


title: Sample 5, Tg, with multifocal lesions

description:
Library name: Sample 5, JELN
JELN5


title: Bulk RNA-seq, gRNA3, BE3, Day4, R1.2

value: Day 4


title: Bulk RNA-seq, gRNA3, BE3, Day4, R2


title: Sample 4, Tg, with multifocal lesions

description:
Library name: Sample 4, JELN
JELN4


title: 230833-RN01

description: Library name: Sample 4


title: 103_P05_H11


title: Sample 2, Tg, with multifocal lesions

description:
Library name: Sample 2, JELN
JELN2


title: 103_P05_H10


title: Sample 3, Tg, with multifocal lesions

description:
Library name: Sample 3, JELN
JELN3


title: Bulk RNA-seq, gRNA3, BE3, Day2, R2

value: Day 2


title: 230831-RN01

description: Library name: Sample 2


title: 230832-RN01

description: Library name: Sample 3


title: Bulk RNA-seq, gRNA3, BE3, Day2, R1


title: Bulk RNA-seq, gRNA2, BE3, Day18, R2


title: Bulk RNA-seq, gRNA3, BE3, Day0, R1

value: Day 0


title: Sample 10, PB, with multifocal lesions

description:
Library name: Sample 10, PB
PB10

source_name: Peripheral Blood

value: Peripheral Blood


title: 103_P05_H09

source_name: Tumor #103


title: 103_P05_H03


title: Sample 15, PB, without lesions

description:
Library name: Sample 15, PB
PB15


title: 103_P05_H02


title: 103_P05_H08


title: Sample 14, PB, without lesions

description:
Library name: Sample 14, PB
PB14


title: 103_P05_H07


title: Bulk RNA-seq, gRNA2, BE3, Day32, R2

value: Day 32


title: Sample 13, PB, without lesions

description:
Library name: Sample 13, PB
PB13


title: KID004C, tumor tissue

city: Yokohama

first: Taku

last: Kouro

state: Kanagawa

address: 2-3-2 Nakao, Asahi-ku

department: Division of Cancer Immunotherapy

country: Japan

institute: Kanagawa Cancer Center Research Institute

description: Library name: KID004C

data_processing:
fastp 0.23.2, STAR 2.7.10b, RSEM v1.2.28
Assembly: GRCh38.113
Supplementary files format and content: text file containing gene_id, transcript_id, length, effective length, expected_count, TPM and FPKM

source_name: stage III ccRCC, female

extract_protocol:
Manufacturer's instructions for Rneasy plus mini was followed.
SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (TaKaRa) was used.

value: Kidney

value: stage III ccRCC

value: female

value: No


title: KID006C, tumor tissue

description: Library name: KID006C


title: Bulk RNA-seq, gRNA2, BE3, Day10, R2

value: mouse embryonic stem cells

value: Day 10


title: 103_P05_H01

data_processing:
We used GATK Best Practices to call mutations from scRNAseq, bWTS and bWES datasets. Depends on the data there are some modifications in the pipeline. Briefly, after trimming and quality control of reads by FastQ (v0.11.9) and Trim Galore (v0.6.5), raw reads were mapped to the mouse genome (GRCm38, mm10) using STAR (v2.7.3a) in two-pass mode which improves the mapping quality at junction sites. Then Picard (v2.22.3) was used for removing duplicated mapped reads and doing indel realignment and base re-calibration. During base quality recalibration, dbSNP variants were used as known sites. In the next step, HaplotypeCaller (v3.8) was used to call the mutations for every single cell separately in GVCF mode. After that, GenotypeGVCFs was used to call the mutations in a joint mode (as pseudo-bulk). These steps keep specificity and sensitivity of calling mutations high. Afterward, the mutations were annotated using ANNOVAR (v2019.10.24). Following that, mutations that were marked as unknown and non-exonic were filtered out. For further confidence, mouse SNPs/Indels filtration was applied to the VCF files based on normal mouse spleen SNPs in addition to a curated in-house database. Finally, somatic-mutations associated with less than 10 reads in at least 2 cells were filtered out. RSEM (v1.3.2) was used to extract expected counts, TPM and FPKM information.
Assembly: mouse mm10
Supplementary files format and content: tab-delimited text files include expression matrix where rows are samples and columns are genes
Supplementary files format and content: tab-delimited text file include all exonic mutations in the samples

extract_protocol: Smart-seq2 (Nature Protocol, 2014, 9: 171)

value: Melanoma cell line-derived tumor

value: HGF-tg C57BL6


title: Sample 11, PB, with multifocal lesions

description:
Library name: Sample 11, PB
PB11

value: with multifocal lesions


title: Bulk RNA-seq, gRNA2, BE3, Day4, R1


title: Multiome, UPN200P, GEX

city: Cincinnati

first: Richard

last: Lu

state: Ohio

institute: CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER

description:
Library name: UPN200P_RNA
UPN200P_filtered_feature_bc_matrix.h5
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence

data_processing:
Demultiplexed scRNA- and scATAC-seq fastq files were input into the Cell Ranger ARC pipeline (version 2.0.0) from 10x Genomics to align reads to the hg38 human reference sequence and generate barcoded count matrices of gene expression and ATAC data.
Demultiplexed data was processed using the Cellranger count pipeline
Assembly: hg38
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5
Supplementary files format and content: CellRanger output files: atac_fragments.tsv.gz

source_name: neuroblastoma

extract_protocol:
Single nuclei were extracted according to the 10X Genomics protocol for Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing. transposed nuclei were combined with Single Cell Multiome ATAC + Gene Expression Gel Beads to generate nanoliter-scale gel bead-in-emulsions (GEMs) on a Chromium Next GEM Chip J
Single-nuclei libraries were generated using the 10x Chromium Single-Cell Instrument and NextGEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics) according to the manufacturer’s protocol.

value: neuroblastoma

value: primary neuroblastoma


title: 103_P05_H06

city: Bethesda

first: Maxwell

last: Lee

institute: National Cancer Institute, NIH

value: CD45-, CD31-, alive, nucleated cells


title: Bulk RNA-seq, gRNA2, BE3, Day4, R1.2

value: Day 4


title: Bulk RNA-seq, gRNA2, BE3, Day18, R1

value: Day 18


title: Sample 12, PB, without lesions

description:
Library name: Sample 12, PB
PB12

value: without lesions


title: 103_P05_H05


title: Sample 7, PB, with multifocal lesions

description:
Library name: Sample 7, PB
PB7

value: Peripheral Blood


title: 103_P05_G12


title: Multiome, UPN2099M, ATAC

description:
Library name: UPN2099M_ATAC
UPN2099M_filtered_feature_bc_matrix.h5
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences

library_source: genomic single cell

value: neuroblastoma metastasis


title: 103_P05_H04


title: Multiome, UPN1177M, GEX

description:
Library name: UPN1177M_RNA
UPN1177M_filtered_feature_bc_matrix.h5
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: Sample 6 PB, with multifocal lesions

description:
Library name: Sample 6 PB
PB6


title: Multiome, UPN3284P, GEX

description:
Library name: UPN3284P_RNA
UPN3284P_filtered_feature_bc_matrix.h5
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: 230830-RN01

description: Library name: Sample 1

value: Papillary Thyroid Carcinoma


title: Sample 9, PB, with multifocal lesions

description:
Library name: Sample 9, PB
PB9


title: Bulk RNA-seq, gRNA2, BE3, Day2, R2

value: Day 2


title: Multiome, UPN2099M, GEX

description:
Library name: UPN2099M_RNA
UPN2099M_filtered_feature_bc_matrix.h5
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: Bulk RNA-seq, gRNA2, BE3, Day10, R1


title: Multiome, UPN2792M, ATAC

description:
Library name: UPN2792M_ATAC
UPN2792M_filtered_feature_bc_matrix.h5
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: Sample 5, PB, with multifocal lesions

description:
Library name: Sample 5, PB
PB5


title: 103_P05_G10


title: Bulk RNA-seq, gRNA2, BE3, Day2, R1


title: Multiome, UPN3284M, ATAC

description:
Library name: UPN3284M_ATAC
UPN3284M_filtered_feature_bc_matrix.h5
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: Sample 8, PB, with multifocal lesions

description:
Library name: Sample 8, PB
PB8


title: Multiome, UPN3284M, GEX

description:
Library name: UPN3284M_RNA
UPN3284M_filtered_feature_bc_matrix.h5
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: Multiome, UPN2792M, GEX

description:
Library name: UPN2792M_RNA
UPN2792M_filtered_feature_bc_matrix.h5
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: 103_P05_G07


title: 103_P05_G09


title: Multiome, UPN200M, GEX

description:
Library name: UPN200M_RNA
UPN200M_filtered_feature_bc_matrix.h5
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: Sample 1, PB, with multifocal lesions

description:
Library name: Sample 1, PB
PB1


title: 103_P05_G11


title: 103_P05_G06


title: 103_P05_G08


title: Sample 3, PB, with multifocal lesions

description:
Library name: Sample 3, PB
PB3


title: Bulk RNA-seq, gRNA2, BE3, Day4, R2


title: Bulk RNA-seq, gRNA2, BE3, Day0, R1

value: Day 0


title: Sample 4, PB, with multifocal lesions

description:
Library name: Sample 4, PB
PB4


title: Sample 2, PB, with multifocal lesions

description:
Library name: Sample 2, PB
PB2


title: Bulk RNA-seq, gRNA1, BE3, Day10, R2


title: Multiome, UPN200M, ATAC

description:
Library name: UPN200M_ATAC
UPN200M_filtered_feature_bc_matrix.h5
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: Bulk RNA-seq, gRNA2, BE3, Day0, R2


title: Bulk RNA-seq, gRNA1, BE3, Day10, R1


title: Bulk RNA-seq, gRNA1, BE3, Day25, R2

value: Day 25


title: Multiome, UPN2045P, ATAC

description:
Library name: UPN2045P_ATAC
UPN2045P_filtered_feature_bc_matrix.h5
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: Multiome, UPN3031P, GEX

description:
Library name: UPN3031P_RNA
UPN3031P_filtered_feature_bc_matrix.h5
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: 103_P05_G05


title: 103_P05_G03


title: Bulk RNA-seq, gRNA1, BE3, Day4, R1.2

value: mouse embryonic stem cells


title: Multiome, UPN3031P, ATAC

description:
Library name: UPN3031P_ATAC
UPN3031P_filtered_feature_bc_matrix.h5
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: Multiome, UPN2045P, GEX

description:
Library name: UPN2045P_RNA
UPN2045P_filtered_feature_bc_matrix.h5
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: 103_P05_G04


title: Bulk RNA-seq, gRNA1, BE3, Day8, R1

value: Day 8


title: Bulk RNA-seq, gRNA1, BE3, Day4, R2


title: Bulk RNA-seq, gRNA1, BE3, Day4, R1


title: Bulk RNA-seq, gRNA1, BE3, Day2, R2


title: Multiome, UPN2855P, ATAC

description:
Library name: UPN2855P_ATAC
UPN2855P_filtered_feature_bc_matrix.h5
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: Multiome, UPN3651P, ATAC

description:
Library name: UPN3651P_ATAC
UPN3651P_filtered_feature_bc_matrix.h5
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: 103_P05_G02

description: Expression_CountValue.tsv,Expression_FPKM.tsv,Expression_TPM.tsv,Mutations.tsv

value: Melanoma cell line-derived tumor


title: ovarian cells, yki3SA, replicate 1

city: San Francisco

first: Todd

last: Nystul

address: 513 Parnassus Ave, Box 0412

institute: UCSF

description: Library name: yki3SA-1

data_processing:
Demultiplexing was performed using CellRanger VERSION, see scRNA-seq EXAMPLE for reference
Assembly: dmel_r6.32
Supplementary files format and content: comma separated file, RNA counts
Supplementary files format and content: comma separated file, cell names, dataset, genotype, UMAP coordinates

organism: Drosophila melanogaster

source_name: adult ovary

growth_protocol: 109-30-Gal4;tub-Gal80ts females were crossed to the respective males (w1118; UAS-armS10; UAS-Ltop4.4;UAS-RasV12;UAS-hepCA;UAS-Hh;UAS-yki3SAS) and offspring was reared at 18°C. Adult F1 offspring was then shifted to 29°C for 14 days and fed wet yeast until dissection.

extract_protocol:
Ovaries were dissected within 30 min in ice cold Schneider’s Insect Medium with 10% FBS and 167 mg/ml insulin on an ice pack. We enriched for the younger, non-vitellogenic stages of the ovary using micro-scissors. Tissue was transferred to an eppendorf tube containing ice-cold Cell Dissociation Buffer (Thermo Fisher Scientific #13151014) and rinsed once with the buffer. Dissociation was performed at RT in Cell Dissociation Buffer with 4 mg/ml elastase (Worthington Biochemical LS002292) and 2.5 mg/ml collagenase (Invitrogen # 17018-029) with nutation and regular pipetting with a P200 to aid tissue dissociation. After 20 min the solution was passed through a 50 μm filter  and the solution incubated for additional 10 min before passage through a 30 μm filter. Enzymes were quenched by adding 500 μl of dissection solution and cells were centrifuged for 5 min at 4 °C and 3500 rcf. Cells were washed in dissection solution and centrifuged again before being resuspended in ice-cold 200 μl PBS with 0.04% ultrapure BSA (Thermo Fisher Scientific AM2616). Dissociation was verified and cells were counted using a cell counting chamber and the solution adjusted to 1000 cells per μl before subjection to single-cell RNA-sequencing.
The library was constructed using the Chromium Single-Cell 3’ Reagent Version 2 Kit (10× Genomics) according to manufacturer's instructions.

value: adult ovary

value: adult ovarian cells

value: temp shifted from 18 to 29°C for 14d and fed with wet yeast


title: ovarian cells, Hh, replicate 2

description: Library name: Hh-2


title: UPN536M_RNA-seq

description: Library name: Sample 18

data_processing:
Basecalling and demultiplexing were performed using bcl2fastq v2.20 software, which is compatible with Illumina NovaSeq 6000 for converting BCL files to FASTQ format.
Sequenced reads were quality-checked using FastQC v0.11.9, trimmed for adaptor sequences and low-quality bases using Trim Galore v0.6.7 (which wraps Cutadapt v3.4), then aligned to the hg19 human reference genome using STAR v2.7.9a with parameters --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate.
Transcript abundances were quantified as Transcripts Per Million (TPM) using Salmon v1.9.0 in alignment-based mode on the STAR output. In brief, reads were quasi-mapped to the transcriptome, with gene-level estimates obtained by summing isoform abundances, normalized for effective length and library size. TPM was converted to FPKM.
Assembly: hg19
Supplementary files format and content: Matrix table with FPKM for every gene and every sample

extract_protocol:
RNA of frozen patient neuroblastoma samples harvested from primary adrenal masses and lymph node/chest wall metastases were extracted using TRIZOL (Life Technologies) followed by purification using a Direct-zol RNA MiniPrep Kit (Zymo Research). RNA-seq libraries were prepared and sequenced by Illumina NovaSeq 6000.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: neuroblastoma

tag: tissue type


title: 103_P05_F09

address: Building 37, Room 5120

value: HGF-tg C57BL6

value: CD45-, CD31-, alive, nucleated cells


title: Multiome, UPN3651P, GEX

description:
Library name: UPN3651P_RNA
UPN3651P_filtered_feature_bc_matrix.h5
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence

value: primary neuroblastoma


title: 103_P05_G01


title: 103_P05_F12


title: UPN2099M_RNA-seq

description: Library name: Sample 17


title: 103_P05_F08


title: ovarian cells, Hh, replicate 1

description: Library name: Hh-1


title: MCF7 cells transfected with SPARC overexpression vector (MCF7 over SPARC) and 5nM Docetaxel treated

type: RNA

city: São Paulo

first: Ana Carolina

last: Pavanelli

state: São Paulo

address: Av Dr Arnaldo, 251

department: CTO

country: Brazil

institute: ICESP

description:
Biological replicate 5. MCF7 cells, SPARC overexpression vector transfected, 5nM docetaxel treated, harvested after 24h of drug exposure.
MCF7SPARC5nM
MCF7overSPARCDOC 5nM

hyb_protocol: 825ng of labeled cRNAs were hybridized with the Human GE 4X44K V2 slides for 17 hours at 65°C. The slides were washed with the GE Wash Buffer 1 and GE Wash Buffer 2 (Agilent), following manufacturer´s instructions.

scan_protocol: Scanned on an Agilent G2600D scanner using the GE2_107_Sep09 protocol.

data_processing: The data quantification and the quality control were performed using the Agilent Feature Extration (v 11.5.1.1) Software.

source_name: MCF7 cell line PAR4 overexpression vector transfected and 100nM docetaxel treated

label_protocol: 162 ng of total RNA (human reference RNA and samples) were primed with 0.8 µl of T7 promoter primer (Agilent) at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of AffinityScript RNA Block Mix (Agilent), and 1 mM of dNTP mix (Agilent). Human RNA reference was labled with Cy3 and samples were labled with  Cy5 at 40°C for 2 h in the presence of T7 RNA polymerase blend (Agilent). The cRNAs were purified using the Qiagen RNeasy mini kit according manufacturer instructions and quantified using NanoDrop (ND-1000).

growth_protocol: MCF7 cells were stably transfected with plasmid pcCMV6-XL6-SPARC expressing the full length SPARC cDNA or with empty vector (pcCMV6-XL6-NEO), both acquired from OriGene (Rockville, MD, USA). Transfection assays were performed using TurboFectin 8.0 transfection reagent according to the manufacturer´s recommendations (OriGene, Rockville, MD, USA). Twenty-four hours after transfection, MCF7 cells were selected with G418 (Gibco, Gaithersburg, MD, USA). The stably transfected MCF7 cells were kept in RPMI 1640 medium supplemented with 10% fetal bovine serum and 800ug/ml G418.

extract_protocol: Total RNA extracted using guanidinium thiocyanate-phenol-chloroform method  according Chomczynsky and Sacchi (1987).

treatment_protocol: MCF7 Neo and MCF7 over SPARC cells were treated with 5nM or 100nM of Docetaxel for a period of 24 hours.

tag: cell line background

value: MCF7 (ATCC® HTB-22™)

value: female breast adenocarcinoma

tag: tumor type

value: Luminal A (Estrogen Receptor positive)

source_name: Agilent's Universal Human Reference RNA

tag: sample type

value: total RNA from 10 human cell lines


title: ovarian cells, hepCA, replicate 2

description: Library name: hepCA-2

tag: cell type


title: MCF7 cells transfected with SPARC overexpression vector (MCF7 over SPARC) and 100nM Docetaxel treated

description:
Biological replicate 6. MCF7 cells, SPARC overexpression vector transfected, 100nM docetaxel treated, harvested after 24h of drug exposure.
MCF7SPARC100nM
MCF7overSPARCDOC 100nM


title: MCF7 cells transfected with the empty vector (MCF7 Neo) and without treatment Replicate 1

description:
Biological replicate 1. MCF7 cells, empty vector transfected (Neo), untreated.
MCF7NEOCTR
MCF7NeoCTR

source_name: MCF7 cell line empty vector transfected and without treatment


title: ovarian cells, yki3SA, replicate 2

description: Library name: yki3SA-2

tag: genotype


title: MCF7 cells transfected with SPARC overexpression vector (MCF7 over SPARC) and without treatment Replicate 1

description:
Biological replicate 4. MCF7 cells, SPARC overexpression vector transfected, untreated.
MCF7SPARCCTR
MCF7SPARCCTR

source_name: MCF7 cell line PAR4 overexpression vector transfected and without treatment


title: MCF7 cells transfected with the empty vector (MCF7 Neo) and 5nM Docetaxel treated

description:
Biological replicate 2. MCF7 cells, empty vector transfected (Neo), 5nM docetaxel treated, harvested after 24h of drug exposure.
MCF7NEO5nM
MCF7NeoDOC 5nM

source_name: MCF7 cell line empty vector transfected and 100nM docetaxel treated


title: MCF7 cells transfected with the empty vector (MCF7 Neo) and 100nM Docetaxel treated

description:
Biological replicate 3. MCF7 cells, empty vector transfected (Neo), 100nM docetaxel treated, harvested after 24h of drug exposure.
MCF7NEO100nM
MCF7NeoDOC 100nM


title: Bulk RNA-seq, gRNA1, BE3, Day0, R1

tag: treatment


title: 103_P05_F06

tag: tissue


title: 103_P05_F10

tag: strain


title: Multiome, UPN2855P, GEX

description:
Library name: UPN2855P_RNA
UPN2855P_filtered_feature_bc_matrix.h5
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: 103_P05_F11

tag: microbiota status


title: UT7_Y1964A

city: Chicago

first: Yong

last: Peng

address: 929 E 57th Street

department: Department of Chemistry

institute: University of Chicago

description:
Library name: Sample_3
5hmC-Seal-seq

data_processing:
Basecalls were performed using bcl2fastq or Illumina nextseq 500 output.
5hmC-Seal-Seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.39, discarding reads left with < 25 bp.
5hmC-Seal-Seq reads were aligned to the GENCODE V40 hg38 genome using BWA-aln version 0.7.17-r1198-dirty. Only uniquely mapping reads with at most two mismatches were retained.
Pea.ks were called uing MACS v2.2.7.1 with the significance cut-off q-value <=0.05
bigWig files were generated using the deepTools.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: UT7 cell

growth_protocol: UT-7 cells were cultured in Iscove’s modified Dulbecco’s medium (IMDM), supplemented with 10% fetal calf serum and 1 U/mL of erythropoietin (EPO).

extract_protocol:
Genomic DNA was harvested using Invitrogen pure link Genomic DNA mini kit.
5hmC-Seal-Seq

value: UT7 cell

value: erythroid progenitor cell lines

value: Y1964 mutant

value: NO


title: ovarian cells, RasV12, replicate 1

description: Library name: RasV12-1


title: E14.5 ureters, Bmp4cKO vs control, rep1

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

institute: Medizinische Hochschule Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended for 4-plex Microarray-Slides in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent Technologies), except that 1000ng of each fluorescently labelled cRNA were used for hybridization.

scan_protocol: Slides were scanned using the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20)

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by use of the extraction protocol file ‘GE2_107_Sep09.xml’.  Measurements of on-chip replicates were averaged using the geometric mean of ‘ProcessedSignal’ (PS) values (for each channel independently) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.  For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:  normalized PSArray i = PSArray i x (1500 / 75th Percentile gPSArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized PS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

source_name: control 1

label_protocol: 200ng of total RNA were used to synthesize AlexaFluor555- or AlexaFluor647- (Invitrogen) labeled cRNA with the ‘Amino Allyl MessageAmp™ II aRNA Amplification Kit’ (#AM1753, Thermo Fisher Scientific) according to the manufacturer’s recommendations, except that the reaction volumes were halved and just one round of T7 amplification was conducted.

extract_protocol: Extraction of total RNA was performed using peqGOLD RNAPure (VWR Peqlab) according to the manufacturer’s recommendations.

treatment_protocol: Ureters were mechanically dissected from E14.5 embryos.

value: NMRI

tag: Sex

value: female

tag: developmental stage

value: ureter

source_name: Bmp4cKO 1


title: E14.5 ureters, Bmp4cKO vs control, rep2

source_name: control 2

value: male

source_name: Bmp4cKO 2


title: UPN1177M_RNA-seq

description: Library name: Sample 16

value: neuroblastoma metastasis


title: 103_P05_F07

value: Melanoma cell line-derived tumor

tag: sorting strategy


title: ovarian cells, hepCA, replicate 1

description: Library name: hepCA-1

value: adult ovary

value: adult ovarian cells

value: temp shifted from 18 to 29°C for 14d and fed with wet yeast


title: UT7_Y1939A

description:
Library name: Sample_2
5hmC-Seal-seq

tag: cell line

value: Y1939 mutant


title: UT7_DM

description:
Library name: Sample_4
5hmC-Seal-seq


title: ovarian cells, Ltop4.4, replicate 2

description: Library name: Ltop4.4-2


title: E14.5 ureters, Smad4cKO (UM) vs control, rep2

source_name: Smad4cKO (UM) 2


title: UPN3284M_RNA-seq

description: Library name: Sample 15

value: neuroblastoma


title: UPN3031M_RNA-seq

description: Library name: Sample 14


title: ovarian cells, Ltop4.4, replicate 1

description: Library name: Ltop4.4-1


title: UT7_WT

description:
Library name: Sample_1
5hmC-Seal-seq

value: WT


title: GM12878-TPT-RNA-Rep2

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

data_processing:
Bulk RNA-seq data were mapped to human reference genome using STAR.
RSEM was used to calculate mRNA count for each gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include mRNA counts for each sample

source_name: blood

extract_protocol:
RNA were extracted with a Trizol-based RNA isolation protocol.
1 μg total RNA were first captured with mRNA capture beads (Vazyme, #N401), then submitted to RNA-seq library preparation kit (Vazyme, NR605). Each sample prepared 2 replicates, and sequenced at Illumina NovaSeq 6000 platform, each sample sequenced to 100 million reads.

value: blood

value: lymphoblastoid

value: Topotecan(topot)


title: 103_P05_F02

value: HGF-tg C57BL6

value: CD45-, CD31-, alive, nucleated cells


title: ovarian cells, armS10, replicate 2

description: Library name: armS10-2


title: ovarian cells, RasV12, replicate 2

description: Library name: RasV12-2


title: E14.5 ureters, Smad4cKO (UM) vs control, rep1

value: NMRI

source_name: Smad4cKO (UM) 1


title: 103_P05_F04

source_name: Tumor #103


title: UPN2113M_RNA-seq

description: Library name: Sample 13


title: 103_P05_E12


title: 103_P05_F05


title: 103_P05_F03


title: UPN3765P_RNA-seq

description: Library name: Sample 7

value: primary neuroblastoma


title: ovarian cells, w1118, replicate 3

description: Library name: w1118-3


title: UPN200M_RNA-seq

description: Library name: Sample 12


title: 103_P05_E11


title: ovarian cells, w1118, replicate 2

description: Library name: w1118-2


title: 103_P05_F01


title: UPN1443M_RNA-seq

description: Library name: Sample 11


title: SC-1

city: Atlanta

first: Linqi

last: Jin

address: 1750 Haygood Dr HSRB II, Floor 4 Room S435

institute: Emory University

description:
Library name: Sample 3
10X Genomics

data_processing:
Raw sequencing reads were demultiplexed and aligned to the GRCh28 human genome using the Cell Ranger (v.7.1.0) pipeline from 10x Genomics. UMI counts were quantified per gene per cell to generate a gene-barcode matrix.
Assembly: Human GRCh38
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.tsv.gz.

source_name: 3D bioprinted cardiac tissue

extract_protocol:
For 2D cell culture, ECs and CMs were dissociated using trypsin-EDTA (0.05%, Thermo Fisher) and TrypLE Select 10X at approximately 95% confluency and resuspended in fresh EC media and CM replating media, respectively. For 3D tissue culture, eHT samples were washed with warm PBS (5 min for 3 times), cut into small pieces, and enzymatically digested by incubation with 4 mg/mL collagenase type I (STEMCELL Technologies) and 1 mg/mL DNase I (STEMCELL Technologies) at 37 °C for 20 min, including 10 min with the addition of TrypLE Select 10X. The digested samples were filtered through a 100 µm cell strainer for up to 3 times to remove the remaining hydrogel residues. After the removal of the dissociation media, cells were resuspended in CM replating medium.
The scRNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3’ Kit (v 3.1) and sequenced on a Novaseq S4 flowcell (Illumina, San Diego, CA, USA) to a mean read depth of at least 54,000 total aligned reads per cell.

value: 3D bioprinted cardiac tissue

value: SCVI-15 and GFP-HUVEC

value: cardiomyocytes, endothelial cells, fibroblasts, and blood cells

value: 3D static coculture, d14


title: 103_P05_E10

value: Melanoma cell line-derived tumor


title: ovarian cells, w1118, replicate 1

description: Library name: w1118-1

value: adult ovary

value: adult ovarian cells


title: 103_P05_E08


title: UPN3728P_RNA-seq

description: Library name: Sample 9

source_name: neuroblastoma


title: ovarian cells, armS10, replicate 1

description: Library name: armS10-1

source_name: adult ovary

value: temp shifted from 18 to 29°C for 14d and fed with wet yeast


title: UPN3770P_RNA-seq

description: Library name: Sample 10

value: neuroblastoma


title: 103_P05_E09


title: GM12878-ETO-RNA-Rep1

value: WT

value: Etoposide(etop)


title: GM12878-TPT-RNA-Rep1

value: blood

value: lymphoblastoid


title: UPN3709P_RNA-seq

description: Library name: Sample 8


title: GM12878-ETO-RNA-Rep2


title: GM12878-TPT-RAD21-CUTTAG-Rep2

data_processing:
CUT&TAG data were processed using the CUT&RUN tools 2.0 (https://github.com/XiangYe-Vandy/CUTRUN_tools) by selecting CUT&TAG (default) as the experiment type.
In brief, raw reads were trimmed tro remove sequencing adapters and mapped to the reference genome using bowtie2.
bigWig files were generated using bamCoverage and normalized with CPM.
Heatmaps and metagene plots were generated using Deeptools (v3.5.2).
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&TAG

extract_protocol:
Cells were dissociated with trypsin and wash twice with 1x PBS at RT.
0.1 million cells were used as input and processed with CUT&Tag kit (Vazyme, TD903) according to the manufacturer’s instructions. RAD21 primary antibody (GeneTex, GTX106012) was used.

value: Topotecan


title: 103_P05_E07

value: HGF-tg C57BL6

value: CD45-, CD31-, alive, nucleated cells


title: UPN3729P_RNA-seq

description: Library name: Sample 6

value: primary neuroblastoma


title: GM12878-DMSO-RNA-Rep1

value: DMSO


title: UPN2099P_RNA-seq

description: Library name: Sample 3


title: ovarian cells, w1118, replicate 4

description: Library name: w1118-4


title: UPN3651P_RNA-seq

description: Library name: Sample 5


title: UPN2538P_RNA-seq

description: Library name: Sample 2


title: GM12878-TPT-RAD21-CUTTAG-Rep1


title: GM12878-DMSO-RNA-Rep2


title: #4 KrasLSL-G12D;Rosa26LSL-tdTomato/LSL-tdTomato;Ptf1aCreER (RNA-seq)

city: Stanford

first: Sofia

last: Ferreira

address: 269 Campus Drive

institute: Stanford University School of Medicine

description:
Library name: BF3069 (KT)
Not represented in norm_counts.csv.

data_processing:
We used 10X Genomics Long Ranger pipeline to map the reads to the mm10 reference mouse genome,
Assembly: Reads were aligned to the GRCm38 mouse genome using HISAT2 (v 2.0.4; RRID:SCR_015530)
Supplementary files format and content: xlsv format, normalized reads

source_name: Pancreatic Ductal Adenocarcinoma

extract_protocol:
RNeasy midi kit (Qiagen, Cat#75144)
Illumina TruSeq RNA Sample Preparation kit (Cat# RS-122-2001) and Illumina HiSeq4000 (RRID:SCR_016386)

value: Pancreatic Ductal Adenocarcinoma

value: Acinar-derived Pancreatic Ductal Adenocarcinoma


title: GM12878-ETO-RAD21-CUTTAG-Rep2

value: Etoposide


title: UPN1443P_RNA-seq

description: Library name: Sample 1


title: 103_P05_E05

value: Melanoma cell line-derived tumor


title: UPN2424P_RNA-seq

description: Library name: Sample 4


title: #5 KrasLSL-G12D;Rosa26LSL-tdTomato/LSL-tdTomato;Ptf1aCreER (RNA-seq)

description:
Library name: CS751 (KT)
Not represented in norm_counts.csv.


title: 103_P05_E04


title: #2 KrasLSL-G12D;Rosa26LSL-tdTomato/LSL-tdTomato;Ptf1aCreER (RNA-seq)

description:
Library name: BF3063 (KT)
Not represented in norm_counts.csv.


title: 103_P05_E06


title: #3 KrasLSL-G12D;Rosa26LSL-tdTomato/LSL-tdTomato;Ptf1aCreER (RNA-seq)

description:
Library name: BF858 (KT)
Not represented in norm_counts.csv.


title: GM12878-ETO-RAD21-CUTTAG-Rep1


title: 103_P05_E02


title: #4 KTC;Trp53fl/fl  (RNA-seq)

description: Library name: BF609 (KPT)

value: KTC;Trp53fl/fl (K= KrasLSL-G12D; T=Rosa26LSL-tdTomato/LSL-tdTomato; C= Ptf1aCreER)