title: NAEC, WheezeRSV2, scRNA-seq

city: chicago

first: Nana-Fatima

last: Haruna

state: Illinois

address: 200 E Chestnut St., Apt 705

department: Department of Medicine, Division of Allergy and Immunology

institute: Northwestern University

description:
Library name: DN15
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
Assembly: hg38
Supplementary files format and content: Rds files of normalized and scaled counts for each sample

source_name: Nasal airway epithelial cells

extract_protocol:
NAECs were collected from the a priori nested cohort of INPSIRE children during a well-child visit between 2-3 years of age. Children were screened for signs and symptoms of respiratory illness, and if detected, visits and collections were rescheduled. NAECs were collected from subjects by brushing nasal passages at the level of the inferior turbinate with a soft flocked cotton swab (Copan, Murrieta, CA, USA) and placing them in cold PneumaCult-Ex Plus Medium (StemCell, Vancouver, Canada).
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, single-cell Gel Beads-in-Emulsion (GEMs) captured cells underwent lysis and transcript barcoding. The corresponding cDNA along with cell barcodes were amplified using PCR. scRNA-seq libraries were constructed using 10x Genomics Library Construction kits (PN-1000196) and Dual Index Kit TT Set A (PN-1000215). The constructed libraries were sequenced on an Illumina platform to generate paired end reads.

value: Nasal airway epithelial cells


title: eBL5

status: Public on Apr 16 2025

type: genomic

city: Ulm

first: Selina

last: Glaser

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University and Ulm University Medical Center

description: endemic Burkitt lymphoma, cryo-preserved, EBV-positive

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation 450 Beadchip using standard Illumina protocol.

scan_protocol: The arrays were scanned using a iScan device.

data_processing: Raw idat files were read into the statistical program R (version 4.3.0) using the minfi package (version 1.46.0). Normalization was performed with the preprocessIllumina() function against the intrinsic controls and without background correction.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: lymph node

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified according to commercially available kits from Qiagen according to standard instructions

tag: tissue

value: lymph node


title: Fracture callus, ADO material, 7 d #1

type: SRA

city: Durham

first: Shyni

last: Varghese

state: NC

address: 203 Research Drive

department: Department of Biomedical Engineering

country: USA

institute: Duke University

description: Calluses harvested 7 days post-treatment

library_source: transcriptomic single cell

data_processing:
10X Genomics reads were converted to FASTQ files using bcl2fastq command-line tool. FASTQ files were aligned to the mm10 reference transcriptome, filtered, and counted using the CellRanger 7.0.0 pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
To obtain single-cell suspensions from calluses of tibiae, mice were euthanized, and calluses were minced using a scalpel in 100 U ml−1DNase I (Millipore Sigma, 10104159001), 1% bovine serum albumin (Sigma-Aldrich) and PBS for 20 min at 37 °C. The cell suspension was filtered using 40-μm cell strainers and centrifuged at 300 g for 5 min and treated with RBC lysis buffer (Millipore Sigma, 11814389001) for 10 min. Cells were stained with propidium iodide and viable cells were sorted using DiVa cell sorter (BD Biosciences) for scRNA-seq preparation.
Cell suspensions harvested from calluses of tibiae were loaded onto a 10x Genomics Chromium Controller Single-Cell Instrument (10x Genomics) mixed with reverse transcription (RT) reagents, gel beads, and oil to generate single-cell gel bead-in emulsions (GEMs). GEM–RT was performed using an Eppendorf Mastercycler Pro using the following program: 53 °C for 45 min, 85 °C for 5 min. After RT, GEMs were broken, and the single-strand cDNA was purified using DynaBeads MyOne Silane Beads (Thermo Fisher Scientific). cDNA was then amplified using the Eppendorf Mastercycler Pro using the following program: 98 °C for 3 min, 11–13 cycles of 98 °C for 15 s, 67 °C for 20 s and 72 °C for 1 min, 72 °C for 1 min. The amplified cDNA product was then purified using the SPRIselect Reagent Kit (0.6 × SPRI; Beckman Coulter). Indexed sequencing libraries were constructed using the reagents in the Chromium Single-Cell Library Kit 3´ v2 using the following steps: 1) fragmentation, end repair and A-tailing, 2) SPRIselect cleanup, 3) adapter ligation, 4) post-ligation cleanup with SPRIselect, 5) sample index PCR, and 6) post-index PCR cleanup. Sequencing libraries were transferred to BGI and were loaded onto a MGISEQ-2000 platform (MGI Tech) for sequencing.

value: Bone marrow

tag: strain

tag: Sex

value: Male

tag: age

value: 20 months

tag: treatment

value: adenosine microgel


title: Pt16Site A_T2

type: RNA

city: Doha

first: Darawan

last: Rinchai

state: Qatar

address: Al Gharrafa St

department: Research

country: Qatar

institute: Sidra Medicine

hyb_protocol: Hybridization was performed at 45°C for 16 hours in a GeneChip Hybridization Oven. Arrays were washed and stained using a GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000, following the Affymetrix protocol.

data_processing:
Raw data were normalized using the Robust Multi-Chip Average (RMA) method in Partek. Probe sets were aggregated into genes and log2-transformed. Gene annotations were matched using the "hugene10sttranscriptcluster.db" R library.
Processed data file contains: the normalized log2-transformed intensity values from the Affymetrix GeneChip Human Gene 1.0 ST Arrays, representing relative gene expression levels.

source_name: tumor biopsy

label_protocol: First- and second-strand cDNA were synthesized from 30 ng of total RNA using the NuGEN Ovation Pico WTA System V2. cDNAs were fragmented, biotinylated with the NuGEN Encore Biotin Module, and hybridized to GeneChip Human Gene 1.0 ST Arrays (Affymetrix).

growth_protocol: Patients with metastatic breast cancer were enrolled and tumor tissue was collected via fine-needle aspiration (FNA) biopsy. Tumors were maintained in a sterile environment until processed for RNA extraction.

extract_protocol: Total RNA was extracted from tumor FNA samples using Qiagen RNA extraction kits (Catalog numbers: 217004/74104). RNA quality was verified using a Nanodrop spectrophotometer and an Agilent 2100 Bioanalyzer.

treatment_protocol: Patients received topical Imiquimod (IMQ) 5% cream, applied 5 days per week for 8 weeks to designated areas. Radiotherapy (RT) was administered to specific tumor regions (30 Gy over five fractions). Cyclophosphamide (200 mg/m²) was given intravenously one week prior to treatment in designated cohorts.

tag: time

tag: local response

value: SD

tag: site

value: Site A

tag: tumor

value: YES

value: CR


title: Compound7_12h, repeat2

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

library_source: transcriptomic

data_processing:
Illumina CASAVA software used for basecalling.
Single-end reads were trimmed for adaptor sequences and aligned to the TAIR10 genome using GSNAP
The HTSeq python tool was used to summarize read counts
R package edgeR was used for statistical analysis
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files generated from HTSeq quantification, contain number of reads

organism: Arabidopsis thaliana

source_name: root meristem

growth_protocol: Col-0 seeds were bleach sterilized and stratified for 24h at 4°C. Seeds were sown on ½ MS medium containing 0.8% agar without sucrose and grown vertically in a growth room at 22°C in continuous light conditions.

extract_protocol:
300 individual root tips were sampled per sample and three biological repeats per time point were used. Root tips were harvested directly into liquid nitrogen, RNA was extracted using the RNeasy kit (QIAGEN).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq® Stranded mRNA Sample Prep Kit.

treatment_protocol: 5 DAG Col-0 plants were transferred to ½ MS plates containing 50μM coral7 and solvent control plates and were sampled at the following time points: 0h, 6h, 12h and 24h.

value: root meristem

tag: cell line

tag: cell type

tag: genotype


title: Pt16Site B_T2

value: Site B

value: NO


title: NAEC, Wheeze2, scRNA-seq

description:
Library name: DN11
10x Genomics


title: eBL45

description: endemic Burkitt lymphoma, cryo-preserved, EBV-negative


title: Fracture callus, CTL material, 7 d #1

value: control microgel


title: NAEC, WheezeRSV1, scRNA-seq

description:
Library name: DN8
10x Genomics


title: Pt17Site B_T2

value: PD


title: NAEC, RSV2, scRNA-seq

description:
Library name: DN5
10x Genomics


title: eBL41


title: 4103570

description: sporadic Burkitt lymphoma, cryo-preserved, EBV-unknown


title: Fracture callus, CTL material, 7 d #2


title: Pt15Site A_T2


title: Pt6Site B_T1

value: PR


title: NAEC, RSV3, scRNA-seq

description:
Library name: DN12
10x Genomics


title: NAEC, Wheeze1, scRNA-seq

description:
Library name: DN3
10x Genomics


title: eBL37


title: NAEC, Control2, scRNA-seq

description:
Library name: DN2
10x Genomics


title: eBL34


title: geAT_15X_6

city: Paris

first: Min Ji

last: Kim

address: 45 rue des saints-Pères

country: France

institute: Inserm 1124

data_processing:
STAR (v2.7.6a), RSEM (v1.3.1) and DESeq2 package
Assembly: Ensembl release 101, Mus_musculus GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM and TPM values for each sample for each sample

source_name: epididymal adipose tissue

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen) after tissue lysis with stainless steel beads of 5 mm (Qiagen) and purified using RNeasy Mini kit (Qiagen).
To construct the libraries, 537 ng of high quality total RNA sample (RIN >7) was processed using Stranded mRNA Prep kit (Illumina) according to manufacturer instructions. Briefly, after purification of poly-A containing mRNA molecules, mRNA molecules are fragmented and reverse- transcribed using random primers. Replacement of dTTP by dUTP during the second strand synthesis will permit to achieve the strand specificity. Addition of a single A base to the cDNA is followed by ligation of Illumina adapters. Libraries were quantified by Q bit and profiles were assessed using the DNA High Sensitivity LabChip kit on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina NovaSeq instrument using 51 base-lengths read in a paired-end mode.

value: epididymal adipose tissue

value: epididymal adipose tissue from mice grafted with fat pad from mice exposed to POP mixture at 15X LOAEL and sacrificed 21 days after


title: NAEC, RSV1, scRNA-seq

description:
Library name: DN4
10x Genomics

value: Nasal airway epithelial cells


title: geAT_15X_2


title: geAT_15X_3


title: geAT_15X_5


title: Pt8Site B_T1


title: Pt31Site B_T1


title: geAT_15X_4


title: NAEC, Control1, scRNA-seq

description:
Library name: DN1
10x Genomics


title: eBL33

value: lymph node


title: Pt30Site B_T1


title: geAT_15X_1


title: Pt15Site B_T2


title: eBL42


title: eBL32


title: 170220-6

city: L'Hospitalet de Llobregat

first: Alessandra

last: Giorgetti

state: Barcelona

address: Avinguda de la Granvia de l’Hospitalet, 199

department: PCMRC

country: Spain

institute: IDIBELL

library_source: genomic

data_processing:
Analysis of data was conducted using the nf-core/sarek (v3.4.2) pipeline implemented in Nextflow (v24.04.0-edge). This pipeline incorporates a comprehensive set of tools for quality control, read alignment, variant calling, and annotation, specifically designed for somatic and germline variant analysis in whole exome sequencing (WES) data.  Raw sequencing reads were pre-processed with Trim Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adapter sequences and low-quality bases, ensuring high-quality input for downstream analysis. Reads were then aligned to the hg19 reference genome using BWA-MEM (19451168). SAMtools (19505943) was employed for sorting, indexing, and filtering of aligned reads, and Picard (https://broadinstitute.github.io/picard/) was utilized for duplicate marking to improve the accuracy of variant calling.  Variant calling was conducted using GATK HaplotypeCaller (20644199) for germline variants and Mutect2 for somatic variants. The generated VCF files were then filtered and annotated with Ensembl’s VEP (27268795), providing functional insights for each variant. Quality control metrics were assessed using MultiQC (27312411) and FastQC (27312411).  A significance threshold of adjusted P value ≤0.05 was used to identify clinically relevant variants.
Assembly: hg19
Supplementary files format and content: Chromosome and position of the Mutect2 result for sample in tab separated file (TSV)

source_name: Peripheral blood

extract_protocol:
Peripheral blood was extracted according the approved protocols at patients clinic or hospital. Peripheral blood DNA was extracted using the manufacturers' protocol (QIAGEN)
Standard Illumina Protocol

value: Peripheral blood


title: Pt27Site B_T1


title: geAT_5X_6

value: epididymal adipose tissue from mice grafted with fat pad from mice exposed to POP mixture at 5X LOAEL and sacrificed 21 days after


title: eBL30


title: 170220-5


title: eBL39


title: Pt26Site B_T1


title: geAT_5X_5


title: Pt5Site B_T1


title: eBL3


title: 170220-4


title: geAT_5X_4


title: Pt25Site B_T1


title: Pt23Site B_T1


title: eBL27


title: eBL25


title: geAT_5X_2


title: Pt22Site B_T1


title: 170220-2


title: 170220-3


title: geAT_5X_3


title: Pt20Site B_T1


title: geAT_5X_1


title: KGN_PARENTAL_Clon sigma

city: Majadahonda

first: Maria

last: Barrero

state: Madrid

address: Crta. Majadahonda-Pozuelo KM 2.2

institute: ISCIII

description: Clon sigma

data_processing:
Fastq files were analyze for quality control using FastQC, v0.11.8
Raw reads were trimmed using Trimmomatic v.0.38 (4-base wide sliding window; removed reads with less than 50 nucleotides)
Read aligment was done with STAR v2.6.1d and quality control performed using RseQC v3.0.0
Gene quatification was calculated using Subread´s featurecounts package v1.6.4
Assembly: hg38
Supplementary files format and content: tab delimited file with gene counts per sample

source_name: KGN cell line

growth_protocol: Parental cell KGN and stablished clones derived from the same cell line were cultured at 37 ͦ C and 5% CO2 in DMEM medium (Dulbecco Modified Eagle Medium) supplemented with 10% bovine fetal serum (FBS) and 1% of penicillin/streptomycin.

extract_protocol:
RNA processing involved TRIzol based isolation method followed by DNAse I treatment.
Libraries were constructed as specified in the TruSeq Stranded Total RNA manufacturer instructions (Illumina)

value: KGN cell line

value: ovarian granulosa

value: FOXL2 WT/C134W

value: Parental clone


title: eBL24


title: Pt17Site B_T1

value: SD

value: YES


title: geAT_Ctrl_6

value: epididymal adipose tissue from mice grafted with fat pad from vehicle-exposed mice and sacrificed 21 days after


title: eBL21


title: KGN_PARENTAL_Clon beta

description: Clon beta


title: Pt16Site B_T1

value: Site B

value: NO

value: CR


title: geAT_Ctrl_5


title: eBL18


title: KGN_PARENTAL_Clon alpha

description: Clon alfa


title: Pt15Site B_T1

value: PD


title: geAT_Ctrl_4

value: epididymal adipose tissue


title: eBL17


title: Pt11Site B_T1


title: geAT_Ctrl_3


title: eBL16


title: KGN_CRISPR_Clon 15

description: Clon 15

value: FOXL2 WT/-

value: CRISPR/Cas9 edited


title: geAT_Ctrl_2


title: Pt8Site A_T1

value: PR

value: Site A


title: Pt6Site A_T1


title: KGN_CRISPR_Clon 8

description: Clon 8


title: eBL10

value: lymph node


title: mCRC_CTC_negative_#3

city: Bursa

first: Dilek

last: Pirim

address: Görükle

country: Turkey

institute: Bursa Uludag University

description: mCRC CTC(-) #3

hyb_protocol: The starting volume of total RNA was 100 ng extracted from peripheral blood and was labelled with cyanine 3-pCp.

scan_protocol: The hybridized slides were scanned using an Agilent SureScan Microarray Scanner (Model G2600D; Agilent Technologies, Inc.) and the images were analyzed by Agilent Feature Extraction (v.12.2.0.7) software (Agilent Technologies, Inc.).

data_processing: The expression data obtained were processed using GeneSpring GX (v.14.9) software (Agilent Technologies, Inc.).

source_name: Whole Blood

label_protocol: MiRNA expression profiles of 24 samples [CTC positive (n=8), CTC negative (n=8) and HIs (n=8)] were analyzed using the Agilent Microarrays (SurePrint G3 Human miRNA r21 8x60K; Cat no. #G4872A Agilent Technologies, Inc.) and miRNA Labelling and Hybridization kit (Agilent Technologies, Inc.) according to the manufacturer's instructions.

growth_protocol: Not applicable.

extract_protocol: Total RNA was isolated from whole blood (600ul) using the miRNeasy Serum/Plasma Advanced kit (QIAGEN GmbH, Hilden, Germany) following the manufacturer’s protocol.

treatment_protocol: Eight ml peripheral venous blood samples were collected from mCRC patients at least seven days after the application of the last therapeutic intervention in EDTA tubes for total RNA isolation and were stored at -20°C until RNA extraction.

tag: disease state

value: CTC negative mCRC

value: Whole Blood


title: gliver_15X_6

source_name: liver

value: liver

value: liver from mice grafted with fat pad from mice exposed to POP mixture at 15X LOAEL and sacrificed 21 days after


title: eBL22


title: KGN_PARENTAL_Clon I

description: Clon I

value: KGN cell line

value: ovarian granulosa

value: FOXL2 WT/C134W

value: Parental clone


title: Human ETMR tumor C19MC amplified

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

description: 10x Genomics

data_processing:
Demultiplexing and preprocessing of the scRNA data was conducted with CellRanger v3.0.2.
After converting the raw 10X data to fastq format with CellRanger's mkfastq, the data was aligned against the human reference transcriptome GRCh38 with the CellRanger count function using default values.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: brain tumor

extract_protocol:
Cell dissociation using papain/DNAse solution, with incubation for 30min for primary tumors and 60min for organoids. Cell dissociation of 2D culture using Accutase and Trypsin EDTA for all conditions. All primary tumor samples were FACS sorted for live cells before taken for scRNA-seq.
Approximately 10,000 vital single-cells of each sample were processed for single-cell RNA sequencing using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, the Chromium Next GEM Chip G and the Single Index Kit T Set A (10X Genomics) according to the manufacturer's instructions. In brief, single-cell GEM (Gel Beads-in-Emulsion) were generated by the Chromium Controller, followed by GEM-RT (reverse transcription), Dynabeads cleanup, cDNA amplification, SPRIselect beads cleanup and Library construction. Quality, purity, size and concentrations of cDNA and libraries were assured by measurement on a Tapestation 2200 (Agilent Technologies). Indexed libraries were sequenced separately by the Illumina NextSeq500 sequencing platform.
scRNA-seq with Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1

value: brain tumor

value: 36 months


title: Pt31Site A_T1

value: YES

value: PD


title: gliver_15X_5


title: Pt30Site A_T1


title: mCRC_CTC_negative_#1

description: mCRC CTC(-) #1


title: Pt27Site A_T1

value: CR


title: gliver_15X_4


title: mCRC_CTC_positive_#2

description: mCRC CTC(+) #2

value: CTC positive mCRC


title: Pt26Site A_T1

value: PR


title: gliver_15X_3


title: mCRC_CTC_positive_#1

description: mCRC CTC(+) #1


title: KGN_CRISPR_Clon 20

description: Clon 20

value: FOXL2 WT/-

value: CRISPR/Cas9 edited


title: gliver_15X_2


title: Pt25Site A_T1

value: Site A


title: geAT_Ctrl_1

value: epididymal adipose tissue

value: epididymal adipose tissue from mice grafted with fat pad from vehicle-exposed mice and sacrificed 21 days after


title: gliver_15X_1

value: liver

value: liver from mice grafted with fat pad from mice exposed to POP mixture at 15X LOAEL and sacrificed 21 days after


title: Pt23Site A_T1

value: SD

value: NO


title: Healthy_Individual_#3

description: HI #3

value: Healthy control

value: Whole Blood


title: mCRC_CTC_negative_#2

description: mCRC CTC(-) #2

value: CTC negative mCRC


title: Healthy_Individual_#2

description: HI #2


title: gliver_5X_6

value: liver from mice grafted with fat pad from mice exposed to POP mixture at 5X LOAEL and sacrificed 21 days after


title: gliver_5X_5


title: Pt20Site A_T1

value: YES

value: PD


title: Pt22Site A_T1

value: CR


title: Healthy_Individual_#1

description: HI #1


title: Healthy_Individual_#8

description: HI #8


title: Colorectal cancer liver metastasis SECA057

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

description: Gene expression estimates from RMA using the Transcriptome Analysis Console (TAC 4.0) software

hyb_protocol: Samples were hybridized onto Affymetrix GeneChip Human Transcriptome 2.0 Arrays (HTA 2.0) according to the manufacturer's protocol (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing: Gene-level expression signals were estimated according to the robust multi-array average (RMA) approach implemented in the Transcriptome Analysis Console (TAC 4.0) software (Affymetrix) with defult settings for background correction and normalization.

label: Biotin

source_name: Liver transplantation patient SECA057

label_protocol: 100 ng total RNA was amplified, fragmented and labelled according to the Affymetrix GeneChip HT WT User Guide.

extract_protocol: Total RNA was extracted from tissue samples using the Allprep DNA/RNA/miRNA Universal kit according to the manufacturer’s instructions (Qiagen GmBH).

value: Colorectal liver metastasis from liver explant

tag: sample with no/low tumor cell content

value: Yes


title: Pt17Site A_T1

value: PR


title: Colorectal cancer liver metastasis SECA056

source_name: Liver transplantation patient SECA056


title: Colorectal cancer liver metastasis SECA054

source_name: Liver transplantation patient SECA054

value: No


title: Colorectal cancer liver metastasis SECA053

source_name: Liver transplantation patient SECA053


title: Colorectal cancer liver metastasis SECA055

source_name: Liver transplantation patient SECA055


title: Pt11Site A_T1

value: Site A


title: gliver_5X_4


title: Colorectal cancer liver metastasis SECA051

source_name: Liver transplantation patient SECA051


title: Healthy_Individual_#7

description: HI #7


title: gliver_5X_3


title: Colorectal cancer liver metastasis SECA049

source_name: Liver transplantation patient SECA049


title: mCRC_CTC_negative_#8

description: mCRC CTC(-) #8


title: Pt16Site A_T1


title: Colorectal cancer liver metastasis SECA052

source_name: Liver transplantation patient SECA052


title: gliver_5X_2


title: mCRC_CTC_negative_#7

description: mCRC CTC(-) #7


title: mCRC_CTC_negative_#6

description: mCRC CTC(-) #6


title: mCRC_CTC_positive_#8

description: mCRC CTC(+) #8

value: CTC positive mCRC


title: Outer hair cells, E18.5, Insm1-KO, rep1

city: Chicago

first: Jaime

last: Garcia-Anoveros

state: IL

address: 303 E Chicago Ave, Ward 10-070, Chicago, IL 60657

department: Anesthesiology

description: Library name: E18.5_Insm1-KO_OHC1

data_processing:
Adaptor sequences were trimmed from reads using Trimmomatic
Trimmed sequences were mapped to GRCm38/mm10 mouse genome using STAR
Read counts were geneated using HTSeq
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts for each gene for each sample

source_name: Organ of Corti

extract_protocol:
Insm1-GFP-Cre positive outer hair cells (OHCs) were FACS-sorted from E18.5 cochleae into 350μL RNA lysis buffer (Qiagen), and RNA was extracted using RNeasy Micro Kit (Qiagen).
Libraries were synthesized by the Beijing Genomics Insititute (BGI) at their facility and the Children's Hospital of Philiadelphia. Genomic DNA was first removed using DNAse I, and ribosomal RNA (rRNA) was removed using RiboZero (Epicentre).The mRNA was fragmented into short fragments of about 200bp. First strand cDNA synthesis was done using random hexamers and the NuGEN Ovation RNA-Amplification System V2. Buffer, dNTPs, RNase H, and DNA polymerase I were added to synthesize the second strand. Double-stranded cDNA was purified with magnetic beads, end reparation and 3′-end single nucleotide A (adenine) addition were performed, and sequencing adaptors were ligated to the fragments, which were enriched by PCR amplification. Libraries were qualified and quantified with an Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR. Libraries were sequenced using the Illumina HiSeq2000 sequencer using 100bp pair-end reads, to a depth of about 50 million reads per sample.

value: Organ of Corti

value: Outer hair cell

tag: developmental stage


title: mCRC_CTC_positive_#7

description: mCRC CTC(+) #7


title: gliver_5X_1

value: liver


title: gliver_Ctrl_6

value: liver from mice grafted with fat pad from vehicle-exposed mice and sacrificed 21 days after


title: Colorectal cancer liver metastasis SECA048

source_name: Liver transplantation patient SECA048


title: mCRC_CTC_positive_#6

description: mCRC CTC(+) #6


title: Outer hair cells, E18.5, Insm1-KO, rep3

description: Library name: E18.5_Insm1-KO_OHC3


title: Outer hair cells, E18.5, Insm1-Het, rep3

description: Library name: E18.5_Insm1-Het_OHC3


title: gliver_Ctrl_5


title: Colorectal cancer liver metastasis SECA045

source_name: Liver transplantation patient SECA045


title: Colorectal cancer liver metastasis SECA046

source_name: Liver transplantation patient SECA046


title: gliver_Ctrl_4


title: Colorectal cancer liver metastasis SECA043

source_name: Liver transplantation patient SECA043


title: Colorectal cancer liver metastasis SECA047

source_name: Liver transplantation patient SECA047


title: Outer hair cells, E18.5, Insm1-KO, rep2

description: Library name: E18.5_Insm1-KO_OHC2


title: Healthy_Individual_#5

description: HI #5

source_name: Whole Blood

value: Healthy control


title: gliver_Ctrl_2

source_name: liver


title: Outer hair cells, E18.5, Insm1-Het, rep1

description: Library name: E18.5_Insm1-Het_OHC1


title: Healthy_Individual_#6

description: HI #6

value: Whole Blood


title: gliver_Ctrl_3


title: Healthy_Individual_#4

description: HI #4


title: Outer hair cells, E18.5, Insm1-Het, rep2

description: Library name: E18.5_Insm1-Het_OHC2


title: eAT_15X_6

source_name: epididymal adipose tissue

value: epididymal adipose tissue

value: epidydimal adipose tissue from mice injected with POP mixture at 15X LAOEL and sacrificed 2 days after


title: Colorectal cancer liver metastasis SECA042

source_name: Liver transplantation patient SECA042


title: gliver_Ctrl_1


title: mCRC_CTC_negative_#5

description: mCRC CTC(-) #5

value: CTC negative mCRC


title: Colorectal cancer liver metastasis SECA044

source_name: Liver transplantation patient SECA044


title: MiNK-215 iNKT cells (with IL-15 transgene), 4-hour FAP+ A375 cells co-culture, donor 2

city: New York

first: Alvaro

last: Sebastian

address: Inc. 149 Fifth Avenue Suite 500

institute: MiNK Therapeutics

description:
Library name: Sample 4
MiNK-215_D02

data_processing:
Adapter trimming was performed with Trim Galore.
Reads were aligned to the human reference genome (GRCh38.p13, Ensembl release 100) using the STAR aligner with gene-level quantification of uniquely mapped reads.
Alignment quality, RNA integrity, and ribosomal content were evaluated using Qualimap and BBDuk.
Assembly: GRCh38.p13, Ensembl release 100
Supplementary files format and content: Tab-delimited text file with raw counts for each sample (columns) and gene (rows)

source_name: iNKT cells

growth_protocol: iNKT cells were cultured in human T cell medium (hTCM) comprising RPMI-1640 (Gibco), 10% (vol/vol) heat-inactivated FBS, 100 U/mL penicillin, 100 μg/mL streptomycin, 10 mM HEPES (Gibco), 1× MEM Amino Acids Solution (Gibco), 1× MEM Non-Essential Amino Acids Solution (Gibco), 50 μM β-mercaptoethanol (Gibco), and 50 U/mL Proleukin (Clinigen Healthcare). Cells were maintained at 37°C in a humidified atmosphere with 5% CO₂. Culture media were refreshed every 2–3 days, and mycoplasma testing was routinely conducted to confirm the absence of mycoplasma contamination throughout the study.

extract_protocol:
Full-length cDNA was synthesized using the SMART-Seq v4 Ultra-Low Input RNA Kit (Takara #634890) following the manufacture's protocol.
Normalized cDNA (120 pg/µl) was used for Illumina-compatible library preparation with the Nextera XT DNA Library Prep Kit (Illumina #FC-131-1024). Libraries were amplified (12 cycles), indexed with Nextera XT DNA dual-index sequences, and purified using 1X SPRI bead clean-up.

treatment_protocol: iNKT cells were co-cultured for 4 hours with A375 cells engineered to express human FAP on the cell surface

value: iNKT cells

value: FAP-CAR & IL15

value: 4-hour FAP+ A375 cells co-culture


title: eAT_15X_5


title: MiNK-215 iNKT cells (with IL-15 transgene), 4-hour FAP+ A375 cells co-culture, donor 1

description:
Library name: Sample 3
MiNK-215_D01


title: FAP-CAR iNKT cells (without IL-15 transgene), 4-hour FAP+ A375 cells co-culture, donor 2

description:
Library name: Sample 2
FAP-CAR-iNKT_D02

value: FAP-CAR


title: mCRC_CTC_negative_#4

description: mCRC CTC(-) #4


title: mCRC_CTC_positive_#5

description: mCRC CTC(+) #5


title: Colorectal cancer liver metastasis SECA039

source_name: Liver transplantation patient SECA039

value: Colorectal liver metastasis from liver explant


title: eAT_15X_3


title: FAP-CAR iNKT cells (without IL-15 transgene), 4-hour FAP+ A375 cells co-culture, donor 1

description:
Library name: Sample 1
FAP-CAR-iNKT_D01


title: eAT_15X_4


title: Colorectal cancer liver metastasis SECA038

source_name: Liver transplantation patient SECA038

value: No


title: eAT_15X_2


title: mCRC_CTC_positive_#4

description: mCRC CTC(+) #4


title: KuDox, no dox, 8days, clone TI

first: Shan

last: Zha

state: NY

address: 1130 Saint Nicholas Ave.

institute: Columbia University

description:
Library name: TI_D8
ribo-depleted RNA sequenced by "Genome Center"

data_processing:
For "AmpSeq" samples, the data were analyzed using STAR2.7.11 and Salmon 1.10.2 to reference transcriptome (Human: GRCh38v44) using standard parameters (maximum number of loci a read can map to as default, and maximum number of multiple alignments allowed as default.
For "Genome center" samples, samples were multiplexed in each lane, which yields a targeted number of paired-end 75 bp reads for each sample. Bases2fastq (version 1.7.0.1196148384) was used for converting BCL files to fastq format, coupled with adaptor trimming. A pseudoalignment to a Kallisto index created from transcriptomes (Human: GRCh38v111) was then performed using Kallisto (0.50.0).
Differential expression analysis was done using DeSeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited .txt file containing estimated gene counts for each sample
Supplementary files format and content: tab-delimited .txt file containing TPMs for each sample

growth_protocol: The HCT116 cells were cultured in McCoy’s 5A medium (Corning 10-050-CV) supplemented with 10% fetal bovine serum (Hyclone SH30071.03), 2 mM L-glutamine (Gibco 25030-081) and penicillin/streptomycin (Gibco 15140-122), and incubated at 37°C. The previously described HEK293 Dox-Ku70 CRISPR KO (clones Sa11, SB, and TI) and control cells were maintained in DMEM medium with 10% fetal bovine serum (Hyclone SH30071.03) supplemented with 1μg/ml doxycycline.

extract_protocol:
RNA was isolated from cells using TRIzol (Invitrogen) following the manufacturer's protocol. RNA quality was determined using the TapeStation System (Agilent) or Bioanalyzer RNA kit (Agilent) and samples with RNA Integrity Number (RIN) higher than 9 were sent for next-generation sequencing (NGS).
For some samples (descirbed as "AmpSeq" in the sample description), poly-A enrichment was used to enrich mRNAs from total RNA samples at day 1, 2, 4, and 6 after IAA&Dox induction, day 2 and 4 after CDK4/6 inhibitor and IAA&Dox induction, and day 4 after 4OHT treatment, then library construction was performed using Illumina TruSeq chemistry and sequenced at AmpSeq. For other samples (described as "Genome Center" in the sample description), ribo-depletion was used to enrich mRNA and non-coding RNA from total RNA samples both before and at 8 days after doxycycline withdrawal. The library construction was performed using Illumina TruSeq chemistry. The final PCR step has been modified using the KAPA HiFi HotStart Ready Mix.The libraries were then sequenced using Element AVITI at Columbia Genome Center.

treatment_protocol: To degrade Ku80 in HCT116 Ku80-AID cells, 0.5 μg/mL doxycycline (Dox, Sigma D9891) and 100 μM indole-3-acetic acid (IAA, Sigma I3750-5G-A) was added to the medium the day after seeding. 50 nM 4OHT final concentration was used to induced Cre-nuclear translocation and Ku86 excision in the HCT116 Ku86flox/-:CreERT2 cells. To deplete Ku70 in the HEK293 Dox-Ku70 CRISPR KO (clones Sa11, SB, and TI) cells, the cells were washed and cultured in doxycycline-free medium.

value: Ku70-/- + doxycycline (Dox)-inducible expression of ectopic Ku75

value: dox withdrawal for 8 days


title: mCRC_CTC_positive_#3

description: mCRC CTC(+) #3

value: CTC positive mCRC


title: eAT_15X_1


title: KuDox, dox, clone TI

description:
Library name: TI_Dox
ribo-depleted RNA sequenced by "Genome Center"

value: Ku70-/- + doxycycline (Dox)-inducible expression of ectopic Ku74

value: dox


title: Colorectal cancer liver metastasis SECA037

source_name: Liver transplantation patient SECA037


title: KuDox, no dox, 8days, clone SB

description:
Library name: SB_D8
ribo-depleted RNA sequenced by "Genome Center"

value: Ku70-/- + doxycycline (Dox)-inducible expression of ectopic Ku73


title: Colorectal cancer liver metastasis SECA034

source_name: Liver transplantation patient SECA034

value: Yes


title: KuDox, dox, clone SB

description:
Library name: SB_Dox
ribo-depleted RNA sequenced by "Genome Center"

value: Ku70-/- + doxycycline (Dox)-inducible expression of ectopic Ku72


title: eAT_5X_5

value: epididymal adipose tissue

value: epidydimal adipose tissue from mice injected with POP mixture at 5X LAOEL and sacrificed 2 days after


title: Colorectal cancer liver metastasis SECA033

source_name: Liver transplantation patient SECA033


title: Knockout, Ketogenic Diet 3

city: Los Angeles

first: Hugo

middle: Jae Mun

state: CA

address: 4760 Templeton St, Unit 3113

department: Neuroscience

institute: UNIVERSITY OF CALIFORNIA, SAN DIEGO

description: Kcna1 Knockout Hippocampus treated with Ketogenic Diet

data_processing:
Demultiplex
DESeq2
Assembly: mm10
Supplementary files format and content: tab delimited counts

source_name: Brain

extract_protocol: Agenta

value: Brain

value: Kcna1 KO

value: Ketogenic Diet


title: eAT_5X_6


title: Knockout, Ketogenic Diet 4


title: Colorectal cancer liver metastasis SECA036

source_name: Liver transplantation patient SECA036


title: Knockout, Ketogenic Diet 2


title: KuDox, dox, clone Sa11

description:
Library name: Sa11_Dox
ribo-depleted RNA sequenced by "Genome Center"

value: Ku70-/- + doxycycline (Dox)-inducible expression of ectopic Ku70


title: eAT_5X_4


title: Colorectal cancer liver metastasis SECA032

source_name: Liver transplantation patient SECA032


title: Ku-AID MAVS, IAA, clone15

description:
Library name: MAVS15_IAA
poly-A enriched RNA sequenced by "AmpSeq"

value: Ku80-AID, MAVS-/-

value: IAA and dox for 4 days


title: Colorectal cancer liver metastasis SECA031

source_name: Liver transplantation patient SECA031

value: Colorectal liver metastasis from liver explant


title: Colorectal cancer liver metastasis SECA029

source_name: Liver transplantation patient SECA029

value: No


title: eAT_5X_2


title: WildType, Ketogenic Diet 4

description: Wildtype animal Hippocampus teated with Ketogenic Diet

value: WT


title: eAT_5X_3


title: Ku-AID MAVS, DMSO, clone15

description:
Library name: MAVS15_DMSO
poly-A enriched RNA sequenced by "AmpSeq"

value: DMSO for 4 days


title: KuDox, no dox, 8days, clone Sa11

description:
Library name: Sa11_D8
ribo-depleted RNA sequenced by "Genome Center"

value: Ku70-/- + doxycycline (Dox)-inducible expression of ectopic Ku71

value: dox withdrawal for 8 days


title: eAT_5X_1


title: eAT_Ctrl_6

value: epidydimal adipose tissue from mice injected with vehicle and sacrificed 2 days after


title: WildType, Ketogenic Diet 2


title: Colorectal cancer liver metastasis SECA023

source_name: Liver transplantation patient SECA023

value: Yes


title: Ku-AID MAVS, DMSO, clone13

description:
Library name: MAVS13_DMSO
poly-A enriched RNA sequenced by "AmpSeq"


title: Knockout, Ketogenic Diet 1


title: WildType, Ketogenic Diet 1


title: eAT_Ctrl_5


title: Colorectal cancer liver metastasis SECA028

source_name: Liver transplantation patient SECA028


title: Knockout, Standard Diet 4

description: Kcna1 Knockout Hippocampus Standard Diet

value: Standard Diet


title: Ku-AID MAVS, DMSO, clone1

description:
Library name: MAVS1_DMSO
poly-A enriched RNA sequenced by "AmpSeq"


title: eAT_Ctrl_3

value: epididymal adipose tissue


title: Knockout, Standard Diet 3


title: eAT_Ctrl_4


title: Colorectal cancer liver metastasis SECA030

source_name: Liver transplantation patient SECA030


title: Colorectal cancer liver metastasis SECA022

source_name: Liver transplantation patient SECA022


title: Colorectal cancer liver metastasis SECA020

source_name: Liver transplantation patient SECA020


title: Ku-AID MAVS, IAA, clone13

description:
Library name: MAVS13_IAA
poly-A enriched RNA sequenced by "AmpSeq"


title: Colorectal cancer liver metastasis SECA019

source_name: Liver transplantation patient SECA019


title: KuCtrl, 4OHT, 4days, rep1

description:
Library name: Ctrl_D4
poly-A enriched RNA sequenced by "AmpSeq"

value: 4OHT for 4 days


title: eAT_Ctrl_2

source_name: epididymal adipose tissue


title: WildType, Ketogenic Diet 3

value: Brain


title: Knockout, Standard Diet 2

value: Kcna1 KO


title: KuCtrl, 4OHT, 4days, rep2

description:
Library name: Ctrl_D4_2
poly-A enriched RNA sequenced by "AmpSeq"


title: Colorectal cancer liver metastasis SECA018

description: Gene expression estimates from RMA using the Transcriptome Analysis Console (TAC 4.0) software

source_name: Liver transplantation patient SECA018


title: Colorectal cancer liver metastasis SECA017

source_name: Liver transplantation patient SECA017


title: Ku-AID MAVS, IAA, clone1

description:
Library name: MAVS1_IAA
poly-A enriched RNA sequenced by "AmpSeq"


title: KuCtrl, EtOH, 4days, rep2

description:
Library name: Ctrl_D0_2
poly-A enriched RNA sequenced by "AmpSeq"

value: EtOH for 4 days


title: Knockout, Standard Diet 1


title: eAT_Ctrl_1


title: WildType, Standard Diet 4

description: Wildtype animal Hippocampus treated with Standard Diet


title: Colorectal cancer liver metastasis SECA016

source_name: Liver transplantation patient SECA016


title: LD-3

city: Ann Arbor

first: Linkang

last: Zhou

state: Michigan

address: Mary Sue Coleman Hall 210 Washtenaw Avenue

institute: University of Michigan

data_processing:
The RNA-seq reads were aligned using the STAR aligner (version 2.7.4a) against the mouse genome assembly release mouse release mouse_GRCm38.p6 from NCBI and gene annotation release M25 from GENCODE. The mapped reads for each gene were quantified using the featureCounts function from the Rsubread package (version 2.0.1)  in the R environment (version 4.0.0).
Assembly: NA
Supplementary files format and content: Text file includes raw counts for each sample

source_name: BMDM

extract_protocol:
The total liver RNA was extracted using RNA extract kit (Invitrogen, Cat: 12183025)
Illumina library prep kit

value: BMDM

value: Wild type

value: Treat with lipid droplets


title: KuCtrl, EtOH, 4days, rep1

description:
Library name: Ctrl_D0
poly-A enriched RNA sequenced by "AmpSeq"


title: Colorectal cancer liver metastasis SECA015

source_name: Liver transplantation patient SECA015

value: Colorectal liver metastasis from liver explant


title: KuCre, 4OHT, 4days, rep2

description:
Library name: Cre_D4_2
poly-A enriched RNA sequenced by "AmpSeq"


title: WildType, Standard Diet 3

source_name: Brain


title: LD-1


title: LD-2


title: WildType, Standard Diet 2


title: KuCre, 4OHT, 4days, rep1

description:
Library name: Cre_D4
poly-A enriched RNA sequenced by "AmpSeq"


title: WildType, Standard Diet 1


title: KuCre, EtOH, 4days, rep2

description:
Library name: Cre_D0_2
poly-A enriched RNA sequenced by "AmpSeq"


title: Colorectal cancer liver metastasis SECA014

source_name: Liver transplantation patient SECA014

value: No


title: TFAP2C KO hEPSC treated with STM2457 , clone 2

city: Ithaca

first: Weiyu

last: Zhang

address: 215 Tower Rd, Biotechnology Building

department: MBG

institute: Cornell University

description: Library name: KO2_STM

data_processing:
Illumina RTA software used for image identification and basecalling.
Raw reads were trimmed using Trim Galore (v0.6.10) , filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs.
Alignment to the human genome (GRCh38 assembly) was performed using Bowtie2 (v2.4.5) with parameter “--very-sensitive”.
Bigwig files were generated by bamCoverage from Deeptools (v3.5.1).
Assembly: hg38
Supplementary files format and content: BigWig file and the ATAC-seq signal

extract_protocol:
50,000 cells were collected and washed twice in pre-cold PBS without DNase. Nuclei were then isolated, lysed and incubated with Tn5 transposase according to manufacturer’s protocol (Vazyme, TD501).
Libraries were prepared by amplifying DNA for 12 cycles using TruePrep DNA Library Prep Kit (Vazyme).

value: embryonic stem cells

value: TFAP2C knockout


title: Control-3


title: Colorectal cancer liver metastasis SECA013

source_name: Liver transplantation patient SECA013


title: Ku-AID, IAA, 6days, clone9

description:
Library name: Ku_9_IAA_D6
poly-A enriched RNA sequenced by "AmpSeq"

value: IAA and dox for 6 days


title: Control-2


title: Control-1


title: TFAP2C KO hEPSC treated with STM2457 , clone 1

description: Library name: KO1_STM


title: Wildtype hEPSC treated with STM2457 , clone 2

description: Library name: WT2_STM

value: Wildtype


title: Colorectal cancer liver metastasis SECA011

source_name: Liver transplantation patient SECA011


title: Ku-AID, IAA, 4days, clone9

description:
Library name: Ku_9_IAA_D4
poly-A enriched RNA sequenced by "AmpSeq"

value: IAA and dox for 4 days


title: FB-Organoid D48 ETMR1 Etoposide 1µM

description: 10x Genomics

data_processing:
Demultiplexing and preprocessing of the scRNA data was conducted with CellRanger v6.0.2.
After converting the raw 10X data to fastq format with CellRanger's mkfastq, the data was aligned against the human+murine reference transcriptome GRCh38-and-mm10-2020-A  with the CellRanger count function using default values.
Assembly: GRCh38-and-mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism:
Homo sapiens
Mus musculus

source_name: organoid

extract_protocol:
Cell dissociation using papain/DNAse solution, with incubation for 60min for organoids. Cell dissociation of 2D culture using Accutase and Trypsin EDTA for all conditions. Organoid samples had consistently > 90% vitality in manual counting, so they were not submitted to FACS sorting.
Approximately 10,000 vital single-cells of each sample were processed for single-cell RNA sequencing using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, the Chromium Next GEM Chip G and the Single Index Kit T Set A (10X Genomics) according to the manufacturer's instructions. In brief, single-cell GEM (Gel Beads-in-Emulsion) were generated by the Chromium Controller, followed by GEM-RT (reverse transcription), Dynabeads cleanup, cDNA amplification, SPRIselect beads cleanup and Library construction. Quality, purity, size and concentrations of cDNA and libraries were assured by measurement on a Tapestation 2200 (Agilent Technologies). Indexed libraries were sequenced separately by the NextSeq2000 sequencing platform.
scRNA-seq with Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1

value: organoid

value: hiPSCs + ETMR_1

value: Etoposide 1µM

tag: treatment time


title: Wildtype hEPSC treated with STM2457 , clone 1

description: Library name: WT1_STM


title: FB-Organoid D48 ETMR1 Carbo 10µM

description: 10x Genomics

value: Carboplatin 10µM


title: Ku-AID, IAA, 2days, clone9

description:
Library name: Ku_9_IAA_D2
poly-A enriched RNA sequenced by "AmpSeq"

value: IAA and dox for 2 days


title: Colorectal cancer liver metastasis SECA008

source_name: Liver transplantation patient SECA008


title: FB-Organoid D48 ETMR1 DMSO

description: 10x Genomics

value: DMSO


title: Ku-AID, DMSO, 2days, clone9

description:
Library name: Ku_9_DMSO
poly-A enriched RNA sequenced by "AmpSeq"

value: DMSO for 2 days


title: Colorectal cancer liver metastasis SECA012

source_name: Liver transplantation patient SECA012


title: Wildtype hEPSC, clone 1

description: Library name: WT1_Control


title: Wildtype hEPSC, clone 2

description: Library name: WT2_Control


title: Colorectal cancer liver metastasis SECA010

source_name: Liver transplantation patient SECA010


title: KuCre, EtOH, 4days, rep1

description:
Library name: Cre_D0
poly-A enriched RNA sequenced by "AmpSeq"

value: EtOH for 4 days


title: FB-Organoid D30 ETMRT3 CP-673451

description: 10x Genomics

value: hiPSCs + ETMR_T3


title: FB-Organoid D30 ETMRT3 DMSO

description: 10x Genomics


title: Colorectal cancer liver metastasis SECA007

source_name: Liver transplantation patient SECA007

value: Yes


title: Colorectal cancer liver metastasis SECA009

source_name: Liver transplantation patient SECA009

value: Colorectal liver metastasis from liver explant


title: Ku-AID, CDKi, 4days, clone9

description:
Library name: Ku_9_CDKi_D4
poly-A enriched RNA sequenced by "AmpSeq"

value: CDK4/6 inhibitor for 4 days


title: Colorectal cancer liver metastasis SECA005

source_name: Liver transplantation patient SECA005

value: No


title: Ku-AID, IAA, 6days, clone7

description:
Library name: Ku_7_IAA_D6
poly-A enriched RNA sequenced by "AmpSeq"


title: Colorectal cancer liver metastasis SECA006

source_name: Liver transplantation patient SECA006


title: FB-Organoid D30 ETMRJ CP-673451

description: 10x Genomics

value: hiPSCs + ETMR_J


title: FB-Organoid D30 ETMRJ DMSO

description: 10x Genomics


title: 24H_R3

city: London

first: Gavin

last: Kelly

state: London

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick institute

data_processing:
Align and quantify by STAR RSEM via nfcore RNASeq pipeline version 3.0
Assembly: Ensembl release 86 of  BDGP6
Supplementary files format and content: Transcript read counts

organism: Drosophila melanogaster

source_name: Wing imaginal discs

growth_protocol: Drosophila melanogasters (fruit flies) were reared on food containing 5.5 g/L agar, 50 g/L glucose, 30 g/L wheat flour, 70 g/L yeast, 4.5 mL/L Propionic acid (Sigma-Aldrich, P5561), 19.5 mL/L Nipagin/Bavistin solution, 2.5 mL/L Penicillin/Streptomycin solution (Sigma-Aldrich, P4333) and ultrapure water. Flies were maintained at 25°C in a Sanyo incubator with 12-hour light/dark cycles.

extract_protocol:
After all the replicates were collected, RNA was extracted using the RNeasy Mini Kit (Qiagen, 74104), following the manufacturer's protocol.
RNA libraries were prepared using the KAPA mRNA HyperPrep Kit (Roche, KK8581), following the manufacturer's protocol.

treatment_protocol: Drosophila larvae were selected at the L2-L3 transition (72 hours after egg laying, which is also recorded time 0) and subsequently allowed to develop for specific periods before the wing imaginal discs were dissected in PBS on ice within 20 min. Wing imaginal discs were then snap-frozen using dry ice and ethanol. Three biological replicates were collected at each time point.

value: Wing imaginal discs

tag: replicate

tag: recoded time


title: Ku-AID, IAA, 4days, clone7

description:
Library name: Ku_7_IAA_D4
poly-A enriched RNA sequenced by "AmpSeq"


title: Colorectal cancer liver metastasis SECA004

source_name: Liver transplantation patient SECA004

tag: tissue


title: Mfap2-/- mouse-4, CCl4 treatment for 8 weeks, bulk RNA-seq

city: Beijing

first: Wei

last: Chen

state: Beijing

address: No. 95 Yong’an road, Xicheng District

department: Beijing Friendship Hospital

country: China

institute: Capital Medical University

description: Sample 8

data_processing:
The HISAT software was used to align clean reads to the mouse genome.
Read counts and FPKM values for each identified gene were calculated using Cufflinks software.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

source_name: liver

growth_protocol: Mfap2+/+ and Mfap2-/- mice

extract_protocol:
Total RNA was extracted from the mouse frozen liver tissues using the RNA simple Total RNA k.
RNA libraries were prepared using the NEBNext Ultra RNA Library Prep Kit.

treatment_protocol: Intraperitoneal injection of CCl4 for 8 weeks

value: liver

value: KO

value: Intraperitoneal injection of CCl4


title: 8H_R3


title: Ku-AID, CDKi+IAA, 4days, clone9

description:
Library name: Ku_9_CDKiIAA_D4
poly-A enriched RNA sequenced by "AmpSeq"

value: CDK4/6 inhibitor, IAA, and dox for 4 days


title: 48H_R2


title: FB-Organoid D30 ETMR1 Etoposide 1µM

description: 10x Genomics

value: organoid

value: hiPSCs + ETMR_1

value: Etoposide 1µM


title: Colorectal cancer liver metastasis SECA002

description: Gene expression estimates from RMA using the Transcriptome Analysis Console (TAC 4.0) software

source_name: Liver transplantation patient SECA002


title: 48H_R3


title: Mfap2-/- mouse-3, CCl4 treatment for 8 weeks, bulk RNA-seq

description: Sample 7


title: FB-Organoid D30 ETMR1 Carbo 10µM

description: 10x Genomics

value: Carboplatin 10µM


title: Mfap2-/- mouse-2, CCl4 treatment for 8 weeks, bulk RNA-seq

description: Sample 6


title: Ku-AID, DMSO, 2days, clone7

description:
Library name: Ku_7_DMSO
poly-A enriched RNA sequenced by "AmpSeq"

value: DMSO for 2 days


title: FB-Organoid D30 ETMR1 CP-673451

description: 10x Genomics


title: 32H_R3


title: 32H_R2


title: Ku-AID, CDKi+IAA, 4days, clone7

description:
Library name: Ku_7_CDKiIAA_D4
poly-A enriched RNA sequenced by "AmpSeq"


title: Colorectal cancer liver metastasis SECA003

source_name: Liver transplantation patient SECA003


title: Colorectal cancer liver metastasis SECA001

source_name: Liver transplantation patient SECA001


title: FB-Organoid D30 ETMR T4 VP-16

description: 10x Genomics

value: hiPSCs + ETMR_T4


title: Mfap2-/- mouse-1, CCl4 treatment for 8 weeks, bulk RNA-seq

description: Sample 5


title: Ku-AID, CDKi, 4days, clone7

description:
Library name: Ku_7_CDKi_D4
poly-A enriched RNA sequenced by "AmpSeq"


title: Mfap2+/+ mouse-4, CCl4 treatment for 8 weeks, bulk RNA-seq

description: Sample 4

value: WT


title: 48H_R1


title: FB-Organoid D30 ETMR T4 Carbo

description: 10x Genomics


title: Ku-AID, IAA, 6days, clone1

description:
Library name: Ku_1_IAA_D6
poly-A enriched RNA sequenced by "AmpSeq"

value: IAA and dox for 6 days


title: Ku-AID, IAA, 2days, clone7

description:
Library name: Ku_7_IAA_D2
poly-A enriched RNA sequenced by "AmpSeq"

value: IAA and dox for 2 days


title: Ku-AID, IAA, 4days, clone1

description:
Library name: Ku_1_IAA_D4
poly-A enriched RNA sequenced by "AmpSeq"

value: IAA and dox for 4 days


title: 32H_R1


title: Mfap2+/+ mouse-2, CCl4 treatment for 8 weeks, bulk RNA-seq

description: Sample 2


title: Mfap2+/+ mouse-1, CCl4 treatment for 8 weeks, bulk RNA-seq

description: Sample 1


title: FB-Organoid D30 ETMR T3 VP-16

description: 10x Genomics

value: hiPSCs + ETMR_T3


title: 8H_R1


title: Ku-AID, DMSO, 2days, clone1

description:
Library name: Ku_1_DMSO
poly-A enriched RNA sequenced by "AmpSeq"


title: FB-Organoid D30 ETMR T3 Carbo

description: 10x Genomics

value: Carboplatin 10uM


title: RBPMS_3_1

city: Boston

first: Haobo

last: Li

state: MA

address: MEDR410 / Lunder Bldg Dock, 255 Charles St

department: Department of Anesthesia, Critical Care, and Pain Medicine

institute: Massachusetts General Hospital and Harvard Medical School

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw sequeence image files from the sequencer were converted to the fastq format and checked for quality: per base sequence quality, the per base sequence content, per base N content, sequence length distribution, adapter and k-mer content and sequence duplication levels are collected for each sequencing run using fastqc.
fastqs are then aligned to the mouse reference genome (mm10) using STAR46 aligner.
Alignment statistics such as average red length, percentage of uniquely mapped reads, percentage of multi-mapped reads and number of splice junctions are collated. Only reads that are uniquely mapped will be considered for read annotation to gene features. Reads are annotated with the ENSEMBL 75 gene transfer format (gtf) file using Salmon.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Endothelial cells

growth_protocol: Endothelial cells were growth in complete mouse endothelial cell medium, with 10% FBS, and 1% PS

extract_protocol:
Cells were harvested and RNA was extacted using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries. Libraries were made with the RiboZero kit followed by the NEB RNA lib kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Endothelial cells were treated with either lentivirus expression empty vector (control) or overexpression of RBPMS for 72 hours

value: Endothelial cells

value: Overexpression

value: 72 hours


title: 3_116

value: Wing imaginal discs


title: Ku-AID, CDKi+IAA, 4days, clone1

description:
Library name: Ku_1_CDKiIAA_D4
poly-A enriched RNA sequenced by "AmpSeq"

value: CDK4/6 inhibitor, IAA, and dox for 4 days


title: 3_112


title: 24H_R2


title: RBPMS_2_1


title: FB-Organoid D30 ETMR T3 DMSO

description: 10x Genomics

value: organoid

value: DMSO


title: Ku-AID, CDKi, 4days, clone1

description:
Library name: Ku_1_CDKi_D4
poly-A enriched RNA sequenced by "AmpSeq"

value: CDK4/6 inhibitor for 4 days


title: RBPMS_1_1


title: Ku-AID, IAA, 24hr, clone9

description:
Library name: Ku_9_IAA_24h
poly-A enriched RNA sequenced by "AmpSeq"

value: IAA and dox for 1 day


title: ETMR_1 CoAgg Organoid D30

description: 10x Genomics

value: hiPSCs + ETMR_1


title: Control_3_1

value: Control


title: Mfap2+/+ mouse-3, CCl4 treatment for 8 weeks, bulk RNA-seq

description: Sample 3

value: liver

value: WT

value: Intraperitoneal injection of CCl4


title: ETMR_J +PC CoAgg Organoid D30

description: 10x Genomics

value: hiPSCs + ETMR_J + mPC


title: FB-Organoid D30 ETMR T4 DMSO

description: 10x Genomics

value: hiPSCs + ETMR_T4


title: Ku-AID, IAA, 2days, clone1

description:
Library name: Ku_1_IAA_D2
poly-A enriched RNA sequenced by "AmpSeq"

value: IAA and dox for 2 days


title: 24H_R1


title: Control_2_1

value: Endothelial cells


title: Ku-AID, CDKi+IAA, 48hr, clone9

description:
Library name: Ku_9_CDKiIAA_48h
poly-A enriched RNA sequenced by "AmpSeq"

value: CDK4/6 inhibitor, IAA, and dox for 2 days


title: Control_1_1

value: 72 hours


title: ETMR_J CoAgg Organoid D30

description: 10x Genomics

value: hiPSCs + ETMR_J


title: 3_88

value: Wing imaginal discs


title: 2_116


title: Forebrain-Organoid D30

description: 10x Genomics

value: organoid

value: hiPSCs


title: Ku-AID, DMSO, 24hr, clone9

description:
Library name: Ku_9_DMSO_24h
poly-A enriched RNA sequenced by "AmpSeq"

value: DMSO for 1 day


title: 2_112


title: A_KD3

description: Endothelial cells

source_name: heart

treatment_protocol: Endothelial cells were treated with either scrambled control (KD-control) or PARP9 siRNA for 72 hours

value: heart

value: endothelial cells

value: PARP9 Knockdown


title: Ku-AID, CDKi, 48hr, clone9

description:
Library name: Ku_9_CDKi_48h
poly-A enriched RNA sequenced by "AmpSeq"

value: CDK4/6 inhibitor for 2 days


title: 2_96


title: Ku-AID, IAA, 24hr, clone1

description:
Library name: Ku_1_IAA_24h
poly-A enriched RNA sequenced by "AmpSeq"

value: IAA and dox for 1 day


title: A_KD2

description: Endothelial cells


title: 2_88


title: ETMR_1 +PC CoAgg Organoid D30

description: 10x Genomics

value: hiPSCs + ETMR_1 + mPC


title: 3_96


title: Ku-AID, DMSO, 24hr, clone1

description:
Library name: Ku_1_DMSO_24h
poly-A enriched RNA sequenced by "AmpSeq"


title: A_KD1

description: Endothelial cells


title: limb_10dpa

type: other

city: Bar Harbor

first: Prayag

last: Murawala

state: ME

address: 159 Old Bar Harbor Rd, Bar Harbor, ME 04609

institute: MDI Biological Laboratory

hyb_protocol: A total of 100 unique genes were included in the analysis of this dataset (10X Xenium Custom panel design: 92QK8P). The custom panel was curated based on previous published single cell analysis datasets (Graber et al. 2018, Leigh et al. 2018 & Zhong et al. 2023), selecting for genes representing molecular markers and genes important in cell signaling, cellular metabolism, cellular communication, extracellular matrix remodeling, structural genes, constitutive genes, and limb patterning. Gene panel probe hybridization, subsequent removal of unbound probes, ligase treatment and final DAPI staining was performed sollowing the 10X Genomics Demonstrated Protocol CG000582.

scan_protocol: Scan protocol initiates by manually selecting regions of interest of the sample. Once consumable reagents and slides are loaded, the instrument's internal sample and liquid handling systems manage the experiment's progress. Data is gathered in cycles consisting of fluorescent probe binding, image capture, and probe removal. Fluorescent intensity points are categorized as potential RNA puncta associated with a corresponding gene ID. All field-of-view images (4240 x 2960 pixels) and their detected transcripts are computationally merged using the DAPI-stained image as a reference. The data was collected using a Xenium Analyzer Instrument running Xenium software version 2.0.1.0 and onboard analysis software version xenium-2.0.0.10. Comprehensive guidance on instrument use and reagent preparation is provided in 10X Genomics’ Demonstrated Protocol CG000582.

data_processing: Information about output files can be found here: https://www.10xgenomics.com/support/in-situ-gene-expression/documentation/steps/onboard-analysis/understanding-xenium-outputs . The analysis is then extended to provide cell segmentation, QC metrics, and summary level analytics including PCA, K-means and graph-based clustering, differential expression, and UMAP dimensionality reduction.

molecule: other

organism: Ambystoma mexicanum

source_name: Ambystoma mexicanum, limb, 10dpa

label_protocol: Tissue washes and decrosslinking was performed to make subcellular RNA targets accesible (10X Genomics Protocol CG000581)

growth_protocol: Axolotls were raised up to 5-cm long (from nouse to tail), and were individually housed in 20% Holtfreter's solution all the time.

extract_protocol: Anesthetized axolotls were amputated at the mid-stylopod level and let them regenerate. For tissue harvesting, the whole stylopod was obtained and immediately embedded in the Tissue-Tek O.C.T. compound (Sakura Finetek), which doesn't affect RNA stability. 15-um cryosections were obtained using a Leica Biosystem CM1860 at -21C, and sections were positioned in the 10X Xenium cryoslides, remembering anteroposterior orientation. Slides with cryosections were stored at -80C for up to one week before following the next steps.

treatment_protocol: All benches, surgical material, and sterescopes were sterilized with Ethanol 70%.

tag: Sex

value: Unknown

tag: strain

value: d/d

value: 15 micrometer cryosection from whole stylopod

tag: regeneration timepoint

value: 10 dpa


title: Ku-AID, CDKi+IAA, 48hr, clone1

description:
Library name: Ku_1_CDKiIAA_48h
poly-A enriched RNA sequenced by "AmpSeq"

tag: treatment

value: CDK4/6 inhibitor, IAA, and dox for 2 days


title: A_Con3

description: Endothelial cells

value: KD-control

tag: time

value: 72 hours


title: 1_112

value: Wing imaginal discs


title: limb_7dpa

source_name: Ambystoma mexicanum, limb, 7dpa

value: 7 dpa


title: Ku-AID, CDKi, 48hr, clone1

description:
Library name: Ku_1_CDKi_48h
poly-A enriched RNA sequenced by "AmpSeq"


title: A_Con2

description: Endothelial cells


title: 1_96


title: limb_3dpa

source_name: Ambystoma mexicanum, limb, 3dpa

value: 3 dpa


title: limb_uninjured

source_name: Ambystoma mexicanum, limb, unninjured

value: 15 micrometer cryosection from whole forelimb

value: 0 (Mature limb)


title: 2022.07.01-DMSO-800_2-2

status: Public on Apr 15 2025

city: Seattle

first: Emily

middle: M

last: Hatch

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

description:
Library name: DMSO_800_2-2
counts_Mpsi1_vs_DMSO.txt

data_processing:
Image analysis and basecalling was performed using Illumina's Real Time Analysis v3.9.25 software, followed by demultiplexing of indexed reads and generation of FASTQ files with Illumina's bcl2fastq-2.20 software.
Salmon 1.2
Sequences mapped to UCSC hg38 with bootstrapping and GC bias correction
Assembly: UCSC hg38
Supplementary files format and content: tab delimited text file includes raw counts for each sample

source_name: hTERT RPE-1

growth_protocol: hTERT RPE-1 cells maintained in F12/DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37 ºC

extract_protocol:
Cells pelleted and snap frozen, extracted using RNAqueous micro kit with DNase I treatment, followed by glycogen precipitation and resuspension in ultra-pure H2O.
Libraries were prepared from total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit and the Nextera XT DNA Library Preparation Kit. Library size distribution was validated using an Agilent 4200 TapeStation.  Additional library QC, blending of pooled indexed libraries, and cluster optimization was performed using Life Technologies’ Invitrogen Qubit® 2.0 Fluorometer.

treatment_protocol: Micronucleation was induced with treatment with 100 nM BAY1217389 for 24 hrs. Where noted, samples were pre-treated for 20 hrs with 10 µM RO-3306.

value: hTERT RPE-1

value: DMSO


title: J259X HCC AVITI

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description:
Library name: sample 2
J259X HCC

data_processing:
BCL basecalling and demultiplexing was performed by spaceranger mkfastq function (10X Genomics)
For each tissue section and corresponding library, the whole slide brightfield image and CytAssist image were aligned manually using the Loupe Browser.
FASTQ and imaging files were imported to Spaceranger count function (10X Genomics) for alignment and gene quantification
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: cell barcode
Supplementary files format and content: features.tsv.gz: gene list
Supplementary files format and content: matrix.mtx.gz: gene by cell expression matrix file
Supplementary files format and content: tissue_hires_image.png: imaging files with high resolution
Supplementary files format and content: tissue_lowres_image.png: imaging files with low resolution
Library strategy: Spatial Transcriptomics

extract_protocol:
The cancer and benign liver regions were identified by a board-certified pathologist. The slides were deparaffinized, Hematoxylin/Eosin stained.
The slides underwent Visium cassette assembly, probe hybridization/ligation, tissue transfer to Visium slide, DNA isolation, clean-up, and ligation probe amplification based on the manufacturer's manual.

value: liver

value: HCC


title: A_Con1

description: Endothelial cells

value: heart

value: endothelial cells


title: 2022.05.18-DMSO-800

description:
Library name: DMSO_800_1
counts_Mpsi1_vs_DMSO.txt


title: 2022.07.01-DMSO-200_2-1

description:
Library name: DMSO_200_2-1
counts_Mpsi1_vs_DMSO.txt


title: 2022.07.01-DMSO-200_2-2

description:
Library name: DMSO_200_2-2
counts_Mpsi1_vs_DMSO.txt


title: 2022.07.01-DMSO-800_2-1

description:
Library name: DMSO_800_2-1
counts_Mpsi1_vs_DMSO.txt


title: 2022.07.01-BAY-800_2-1

description:
Library name: BAY_800_2-1
counts_Mpsi1_vs_DMSO.txt


title: limb_14dpa

source_name: Ambystoma mexicanum, limb, 14dpa

value: Unknown

value: d/d

value: 14 dpa


title: 2022.07.01-BAY-200_2-1

description:
Library name: BAY_200_2-1
counts_Mpsi1_vs_DMSO.txt


title: 1_116


title: 2022.05.27-iMN-800

description:
Library name: 8_2_iMN_3
counts_rMN+_vs_rMN-.txt


title: 2022.05.18-BAY-800

description:
Library name: BAY_800_1
counts_Mpsi1_vs_DMSO.txt


title: 2022.07.01-BAY-800_2-2

description:
Library name: BAY_800_2-2
counts_Mpsi1_vs_DMSO.txt


title: 2022.05.18-DMSO-200

description:
Library name: DMSO_200_1
counts_Mpsi1_vs_DMSO.txt


title: 2022.07.01-BAY-200_2-2

description:
Library name: BAY_200_2-2
counts_Mpsi1_vs_DMSO.txt


title: limb_5dpa

source_name: Ambystoma mexicanum, limb, 5dpa

value: 15 micrometer cryosection from whole stylopod

value: 5 dpa


title: 2022.05.27-dMN-200

description:
Library name: 8_2_dMN_3
counts_rMN+_vs_rMN-.txt


title: 2022.05.26-dMN-200

description:
Library name: 8_2_dMN_2
counts_rMN+_vs_rMN-.txt


title: 2022.05.25-iMN-800

description:
Library name: 8-2_iMN_1
counts_rMN+_vs_rMN-.txt


title: 2022.05.25-dMN-200

description:
Library name: 8-2_dMN_1
counts_rMN+_vs_rMN-.txt


title: 2022.05.18-BAY-200

description:
Library name: BAY_200_1
counts_Mpsi1_vs_DMSO.txt


title: 2022.05.26-iMN-800

description:
Library name: 8_2_iMN_2
counts_rMN+_vs_rMN-.txt


title: 2022.04.14-MN1-800_r1

description:
Library name: 800-200_MN-yes_r1
counts_MN+_vs_MN-.txt


title: 2022.04.14-MN1-800_r2

description:
Library name: 800-200_MN-yes_r2
counts_MN+_vs_MN-.txt


title: 1_88


title: J259B HCC+adjacent AVITI

description:
Library name: sample 1
J259B HCC+adjacent

value: HCC+adjacent


title: 2022.04.14-MN0-200_r1

description:
Library name: 800-200_MN-no_r1
counts_MN+_vs_MN-.txt


title: 2022.04.14-MN1-200_r2

description:
Library name: 200-800_MN-yes_r2
counts_MN+_vs_MN-.txt


title: 2022.04.14-MN1-200_r1

description:
Library name: 200-800_MN-yes_r1
counts_MN+_vs_MN-.txt


title: 2022.04.14-MN0-800_r1

description:
Library name: 200-800_MN-no_r1
counts_MN+_vs_MN-.txt


title: 2022.04.14-MN0-800_r2

description:
Library name: 200-800_MN-no_r2
counts_MN+_vs_MN-.txt


title: 2022.03.18-MN1-800

description:
Library name: 800-200_MNated
counts_MN+_vs_MN-.txt


title: 2022.03.18-MN0-200

description:
Library name: 800_200_not
counts_MN+_vs_MN-.txt


title: Molino ovary 2

city: Kansas City

first: Di

last: Wu

state: MO

institute: Stowers Institute for Medical Research

description:
Library name: L65102
10x Genomics

data_processing:
Cell Ranger v7.1.0 was used to process the data. Raw reads were demultiplexed into Fastq format using cellranger mkfastq. Alignment, filtering, barcode counting, and UMI counting was done using cellranger’s count pipeline.
Assembly: Astyanax_mexicanus-2.0 (Annotation: Ensembl 110)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Astyanax mexicanus

source_name: Ovary

extract_protocol:
The digestive enzyme mixture is composed of 3 mg/ml collagenase I (C0130, Sigma-Aldrich), 3 mg/ml collagenase II (C6885, Sigma-Aldrich) and 1.6 mg/ml hyaluronidase (H4272, Sigma-Aldrich) in L15 media (112-029-101, Quality Biological). Fish were fasted one day before cell dissociation. Each sample and library were collected and constructed from a single fish, and the fish being used were aged-matched.  The left side ovary from one adult fish was dissected and stored on ice in an RNA Lobind tube (0030108310, Eppendorf north america) containing 3 ml of L15 for no more than 40 min. Tissues were minced with dissection scissors into pieces. L15 media were replaced with 3 ml of digestive enzyme mixture after the tissue settled down to the bottom of the tube. Samples were incubated on an orbitron rotator (260200, Boekel Scientific) at room temperature until no obvious cell clumps were observed (35~45 min, depending on samples). Cells were centrifuged at 300 g for 3 min at 4 °C, resuspended in 3 ml of TrypLE (12604021, ThermoFisher Scientific) and incubated on the orbitron rotator at room temperature for 15 min. 3 ml of 20% FBS (SH30071.03E, Cytiva) in L15 were added to the cell suspensions and incubated on the orbitron rotator at room temperature for 1 min to stop TrypLE reaction. Cell suspensions were then added with 15 ml of L15 and centrifuged at 300 g for 3 min at 4 °C to get the cell pellets. The cell pellets were resuspended and washed three times with 5 ml of L15 using a P1000 pipette and centrifuged at 300 g for 3 min. Cell pellets were resuspended in 2 ml L15 and filtered through a 70 µm nylon filter (352350, Corning) and then through a 40 µm nylon filter (352340, Corning) into Lobind tubes to remove large cells and cell clumps. The filters were washed twice with 2 ml L15. The filtrates were centrifuged at 300 g for 3 min and resuspended in 1 ml of 2% BSA (A9418, Sigma-Aldrich) in phosphate-buffered saline (PBS) (20012050, ThermoFisher Scientific) and transferred into Lobind tubes.
scRNA-seq libraries were prepared by Stowers Sequencing core. Dissociated, sorted cells were assessed for concentration and viability using a Luna-FL cell counter (Logos Biosystems). Cells deemed to be at least 84% viable were loaded based on live cell concentration onto a Chromium iX Series instrument (10x Genomics) and libraries prepared using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics) according to manufacturer’s directions. Resulting cDNA and short fragment libraries were checked for quality and quantity using a 2100 Bioanalyzer (Agilent Technologies) and Qubit 2.0 Fluorometer (Thermo Fisher Scientific). With cells captured estimated at ~1,100-5,500 cells per sample, libraries were pooled and sequenced to a depth necessary to achieve at least 38,000 mean reads per cell on an Illumina NextSeq 2000 instrument utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths 28*10*10*90bp.

value: Ovary

value: WT

value: Non-treated


title: U87-MG cells, HAM rapid, replicate 1, hour 24

city: Rio de Janeiro

first: Otávio

middle: de Melo

last: Espíndola

state: RJ

address: Av. Brasil, 4365

country: Brazil

institute: FIOCRUZ

description: Library name: HAMr1_24h

data_processing:
STAR v2.7.5c was used to align the trimmed and paired reads to the human genome version GRCh38.p14, using the GFF3 annotation file (version GRCh38.106) from Ensembl.
Samtools v1.10 was employed to sort and index the resulting BAM files.
FeatureCounts v2.0.1 was used to generate a transcript count table.
Assembly: GRCh38.p14
Supplementary files format and content: Text flie containing raw counts generated by featureCounts.

source_name: Brain

extract_protocol:
Total RNA was extracted with the PureLink™ RNA Micro Scale kit (Invitrogen, USA), following the manufacturer’s instructions.
Paired-end genomic libraries of enriched mRNAs were constructed with the Stranded mRNA Prep kit (Illumina) and the Illumina RNA UDI A LIG 96 indexes (IDT Technologies) according to the manufacturer’s instructions.

treatment_protocol: U87-MG cells were cultured in triplicates at 2×105 cells/well in 24-well plates in 500µl of complete DMEM and treated for 6h or 24h with 25% v/v of pooled CSF from patients categorized as HAC, HAMvs, HAMt, or HAMr, and untreated cells were used as a negative control.

value: Brain

value: Glioblastoma


title: U87-MG cells, HAM typical, replicate 3, hour 24

description: Library name: HAMt3_24h


title: U87-MG cells, asymptomatic, replicate 3, hour 24

description: Library name: HAC3_24h


title: U87-MG cells, HAM rapid, replicate 2, hour 24

description: Library name: HAMr2_24h


title: U87-MG cells, HAM very slow, replicate 2, hour 24

description: Library name: HAMvs2_24h


title: U87-MG cells, HAM rapid, replicate 3, hour 24

description: Library name: HAMr3_24h


title: U87-MG cells, asymptomatic, replicate 2, hour 24

description: Library name: HAC2_24h


title: U87-MG cells, HAM typical, replicate 2, hour 24

description: Library name: HAMt2_24h


title: U87-MG cells, HAM typical, replicate 1, hour 24

description: Library name: HAMt1_24h


title: U87-MG cells, HAM very slow, replicate 1, hour 24

description: Library name: HAMvs1_24h


title: Molino ovary 1

description:
Library name: L65101
10x Genomics


title: U87-MG cells, HAM very slow, replicate 3, hour 24

description: Library name: HAMvs3_24h


title: Pachón ovary 2

description:
Library name: L64998
10x Genomics


title: U87-MG cells, untreated, replicate 3, hour 24

description: Library name: UT3_24h


title: Pachón ovary 1

description:
Library name: L64997
10x Genomics


title: U87-MG cells, asymptomatic, replicate 1, hour 24

description: Library name: HAC1_24h


title: Surface fish ovary 2

description:
Library name: L64221
10x Genomics


title: U87-MG cells, untreated, replicate 2, hour 24

description: Library name: UT2_24h


title: M KO 4

city: Minneapolis

first: Emilyn

last: Alejandro

state: MN

address: 2231 6th Street SE

institute: University of Minnesota

description: Library name: 18_S9

data_processing:
The  University of Minnesota Research Informatics at MSI  analyzed the RNA Seq output. 2 x 50bp FastQ paired-end reads for 17 samples  were trimmed using Trimmomatic (v 0.33) enabled with the optional headcrop 3 and  “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.
Quality control on raw sequence data for each sample was performed with FastQC.
Sequencing reads were mapped to the mouse reference genome (Mus_musculus.GRCm39.109.gtf) using Hisat2.
Differentially expressed genes  were calculated using edgeR software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: Mus_musculus.GRCm39.109.gtf

source_name: Whole placenta

growth_protocol: Embryonic 17.5 collection; frozen in liquid nitrogen

extract_protocol:
Total RNA was extracted in TRIzol reagent and column purified with DNAse treatment using the Purelink RNA mini kit as per manufacturer's instructions
RNA-seq: Dual-indexed libraries were generated using the TruSeq stranded mRNA library kit

treatment_protocol: Cyp19-cre mediated excision of MCU (MCU flox/flox)

value: Whole placenta

value: Male

value: Pl-MCUKO


title: U87-MG cells, untreated, replicate 1, hour 24

description: Library name: UT1_24h


title: Surface fish ovary 1

description:
Library name: L64220
10x Genomics


title: M Ctrl 4

description: Library name: 17_S8

value: Ctrl


title: 2022.03.18-MN1-200

description:
Library name: 200-800_MNated
counts_MN+_vs_MN-.txt

value: hTERT RPE-1


title: M Ctrl 3

description: Library name: 16_S7


title: U87-MG cells, HAM rapid, replicate 2, hour 6

description: Library name: HAMr2_6h


title: 2022.03.18-MN0-800

description:
Library name: 200-800_not
counts_MN+_vs_MN-.txt


title: U87-MG cells, HAM rapid, replicate 3, hour 6

description: Library name: HAMr3_6h


title: GR-null kidney E18.5 replicate 3

city: Melbourne

first: Mehran

last: Piran

state: VIC

address: 19 Innovation Walk

department: Anatomy and Developmental Biology

country: Australia

institute: Monash University

description:
Library name: Sample7
N3

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data
Firstly, reference genome sequences and gene model annotation files of relative species (GRm39.97) were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data

source_name: Kidney

extract_protocol:
Total RNA of each sample was extracted using TRIzol reagent (Invitrogen) following the manufacturer's instructions.
Next generation sequencing library preparations were constructed according to the manufacture's protcol. The The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double_x0002_stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA_x0002_tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor_x0002_ligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic, Taiwan, China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

value: Kidney

value: GR-null


title: U87-MG cells, HAM rapid, replicate 1, hour 6

description: Library name: HAMr1_6h


title: M Ctrl 2

description: Library name: 15_S6


title: U87-MG cells, HAM typical, replicate 3, hour 6

description: Library name: HAMt3_6h


title: U87-MG cells, HAM very slow, replicate 3, hour 6

description: Library name: HAMvs3_6h


title: M KO 2

description: Library name: 13_S4


title: M KO 3

description: Library name: 14_S5


title: WT kidney E18.5 replicate 4

description:
Library name: Sample4
C4


title: GR-null kidney E18.5 replicate 2

description:
Library name: Sample6
N2


title: U87-MG cells, HAM very slow, replicate 2, hour 6

description: Library name: HAMvs2_6h


title: M Ctrl 1

description: Library name: 12_S3


title: M KO 1

description: Library name: 11_S2


title: U87-MG cells, asymptomatic, replicate 1, hour 6

description: Library name: HAC1_6h


title: GR-null kidney E18.5 replicate 1

description:
Library name: Sample5
N1


title: WT kidney E18.5 replicate 2

description:
Library name: Sample2
C2


title: U87-MG cells, HAM typical, replicate 1, hour 6

description: Library name: HAMt1_6h


title: WT kidney E18.5 replicate 3

description:
Library name: Sample3
C3


title: U87-MG cells, HAM very slow, replicate 1, hour 6

description: Library name: HAMvs1_6h


title: U87-MG cells, untreated, replicate 2, hour 6

description: Library name: UT2_6h


title: WT kidney E18.5 replicate 1

description:
Library name: Sample1
C1


title: U87-MG cells, untreated, replicate 3, hour 6

description: Library name: UT3_6h


title: U87-MG cells, asymptomatic, replicate 3, hour 6

description: Library name: HAC3_6h


title: F Ctrl 5

description: Library name: 8_S17

value: Female


title: F KO 4

description: Library name: 10_S1


title: DM

city: Chengdu

first: Siyu

last: Long

state: China Sichuan

address: Yihuan street

institute: Sichuan University

description: Library name: sample 3

data_processing:
Sequencing data for each sample were aligned to the mouse reference genome rattus_norvegicus__ensembl-97 using CellRanger v7.1.0 (https://www.10xgenomics.com/support/software/cell-ranger) to facilitate cell identifi-cation and expression matrix construction.
Assembly: rattus_norvegicus__ensembl-97
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: bone

extract_protocol:
Single-cell suspensions were prepared according to the protocol of Chromium Single Cell 3’Solution (V3 chemistry). All specimens were washed two times with cold 1x phosphate-buffered saline (PBS) .Haemocytometer (Thermo Fisher Scientific) was used to evaluate cell viability rates.Then, we used Countstar to count the concentration of sinale-cell suspension and adiust the concentration to1000 cells/ul. Samples that were lower than the required cell concentration defined in the user guide (i.e., <400 cells/ul) were pelleted and re-suspended in a reduced volume, and then the concentration of the new solution was counted again.
Single-cell RNA sequencing (scRNA-seq) libraries were constructed using the 10x Chromium Single Cell 3’ platform (10X Genomics, Pleasanton, CA, USA) according to the manufacturer’s protocol. Briefly, single-cell suspensions were loaded onto a Chro-mium microfluidic chip to generate single-cell Gel Beads in Emulsion (GEMs). The scRNA-seq libraries were then prepared using the Chromium Single Cell 3’ Reagent Kit v3.1 (10X Genomics, Pleasanton, CA, USA). Library quality was assessed using the Ag-ilent 2100 Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA), and se-quencing was performed on the Illumina NovaSeq 6000 platform (Illumina, San Di-ego, CA, USA) with a sequencing depth of at least 50,000 reads per cell.

value: bone

value: bone cells

value: osteocytes

value: scaffold implantation


title: FTO-WT-RNA-seq-3

city: xian

first: Cangang

state: State...

address: Yanta district, xi 'an city, shaanxi province

institute: xian jiaotong university

data_processing:
The raw reads were trimmed by using Trim Galore with default parameters. After removing low-quality bases RNAs, the clean data were mapped to mouse genome (GRCm39) using Hisat2 RNA-Seq alignment software, and unique reads were retained to quantify gene expression counts from bam files by using featurecounts . The raw counts were calculated into TPM(Trancripts per million).
Sequencing reads were mapped to the mouse reference genome (mm39) using HISAT2. m6A-enriched peaks and diff peaks were identified by exomePeak2 with the corresponding input sample as control. HOMER was used for de novo followed by localization of the motif with respect to peak summit.m6A peaks were visualized using Integrative Genomics Viewer software.
Assembly: mm39

source_name: spleen

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA concentration was detected by the Qubit RNA broad range assay in the Qubit Fluorometer (Invitrogen)
After quality control using an RNase-free agarose gel and Agilent 2100 (Agilent Technologies, Palo Alto, CA, USA), RNA-Seq libraries were prepared using 200 ng total RNA with TruSeq RNA sample prep kit (Illumina). Oligo(dT)-enriched mRNAs were fragmented randomly with fragmentation buffer, followed by the first- and second- strand cDNA synthesis.
After a series of terminal repair, the double-stranded cDNA library was obtained through PCR enrichment and size selection. The prepared cDNA library was sequenced with the Illumina Hiseq 2000 sequencer (Illumina HiSeq 2000 v4 Single-Read 50 bp) after pooling according to its expected data volume and effective concentration

value: spleen

value: FTO-WT


title: U87-MG cells, untreated, replicate 1, hour 6

description: Library name: UT1_6h


title: F KO 3

description: Library name: 7_S16


title: U87-MG cells, HAM typical, replicate 2, hour 6

description: Library name: HAMt2_6h


title: FTO-WT-RNA-seq-2


title: U87-MG cells, asymptomatic, replicate 2, hour 6

description: Library name: HAC2_6h


title: MRC5 iN 48h NGF 10 nM rep 1

first: Damien

last: Detraux

state: Washington

address: 850 Republican St

institute: University of washington

description:
Library name: Sample 7
Column name in Normalized_counts_wholeRNAseq.txt: iN +NGF 1

data_processing:
All fatsq files processing were performed using Partek Flow sequencing from Illumina.
Bases were trimmed using Quality score of min 35, trimmed from 3' end
Read counts were aligned using STAR - 2.7.8a and quantified to annotation model (Partek E/M) and normalized using Median ratio
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

growth_protocol: Human lung fibroblasts (MRC5; ATCC #CCL-171) were cultured in DMEM High glucose with Glutamax (Gibco, 10564011) supplemented with 1/100 penicillin-streptomycin (Gibco, 15140–122) and 10% FBS (Biowest). At day 0 and until D16 the media was switched to induction media composed of a base of a 1:1 mixture of DMEM/F12 (Gibco, 31330–038) and Neurobasal Medium (Gibco, 21103–049) supplemented with 1 x N-2 Supplement (Gibco, 17502–048), 1 x B-27 Supplement (Gibco, 17504–044) and 1/100 penicillin-streptomycin (Gibco, 15140–122). This base is supplemented with 2 µg/ml doxycycline, 1 µg/ml laminin (Santa Cruz biotechnologies), 500 µg/ml dibutyryl cAMP (Santa Cruz Biotechnologies), 150 ng/ml Noggin (SinoBiologicals), 0.5 µM LDN193189 and 0.5 µM A83-01, 3 µM CHIR99021, 5 µM forskolin and 10 µM SB-431542, all from Medchemexpress.

extract_protocol:
Total RNA was extracted using the Promega Aurum total RNA kit
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: At day 14 10 nM of NGF or 237 agonist were added to fresh induction medium and maintained 48h

value: Induced neuron

value: ASCL1:NGN2 OE

value: NGF 10nM


title: MRC5 iN 48h NGF 10 nM rep 3

description:
Library name: Sample 9
Column name in Normalized_counts_wholeRNAseq.txt: iN +NGF 3


title: F Ctrl 4

description: Library name: 5_S14

value: Whole placenta


title: F KO 2

description: Library name: 6_S15


title: MRC5 iN 48h NGF 10 nM rep 2

description:
Library name: Sample 8
Column name in Normalized_counts_wholeRNAseq.txt: iN +NGF 2


title: MRC5 iN 48h 237 10 nM rep 2

description:
Library name: Sample 5
Column name in Normalized_counts_wholeRNAseq.txt: iN +237 2


title: MRC5 iN 48h 237 10 nM rep 3

description:
Library name: Sample 6
Column name in Normalized_counts_wholeRNAseq.txt: iN +237 3


title: F Ctrl 3

description: Library name: 4_S13


title: FTO-KO-RNA-seq-3

value: FTO-KO


title: FTO-KO-RNA-seq-2


title: F KO 1

description: Library name: 3_S12

value: Pl-MCUKO


title: MRC5 iN Vehicle control rep 1

description:
Library name: Sample 1
Column name in Normalized_counts_wholeRNAseq.txt: iN Control 1

value: Control


title: MRC5 iN 48h 237 10 nM rep 1

description:
Library name: Sample 4
Column name in Normalized_counts_wholeRNAseq.txt: iN +237 1


title: FTO-KO-RNA-seq-1


title: F Ctrl 2

description: Library name: 2_S11

value: Ctrl


title: MRC5 iN Vehicle control rep 3

description:
Library name: Sample 3
Column name in Normalized_counts_wholeRNAseq.txt: iN Control 3


title: Brain-slides-HD01_n3

city: Uppsala

first: Peetra

middle: Ulrica

last: Magnusson

address: Dag Hammarskjoldsv 20

department: Immunology, Genetics and Pathology (IGP)

country: Sweden

institute: Uppsala University

description: Library name: Brain-slides-HD01_3

data_processing:
The raw sequence data was processed by using the nf-core/rnaseq pipeline, version 3.3.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: iPSCs HD_01

extract_protocol:
Total RNA was isolated using the RNeasy Kit (Qiagen)
TruSeq stranded mRNA libraries (Illumina)

value: iPSCs HD_01

value: iPSCs-derived endothelial cells

value: WT


title: m6A-WT-IP

data_processing:
The raw reads were trimmed by using Trim Galore with default parameters. After removing low-quality bases RNAs, the clean data were mapped to mouse genome (GRCm39) using Hisat2 RNA-Seq alignment software, and unique reads were retained to quantify gene expression counts from bam files by using featurecounts . The raw counts were calculated into TPM(Trancripts per million).
Sequencing reads were mapped to the mouse reference genome (mm39) using HISAT2. m6A-enriched peaks and diff peaks were identified by exomePeak2 with the corresponding input sample as control. HOMER was used for de novo followed by localization of the motif with respect to peak summit.m6A peaks were visualized using Integrative Genomics Viewer software.
Assembly: mm39
Library strategy: m6A-seq


title: FL

description: Library name: sample 2

value: bone


title: MRC5 iN Vehicle control rep 2

description:
Library name: Sample 2
Column name in Normalized_counts_wholeRNAseq.txt: iN Control 2


title: Brain-slides-HD01_n2

description: Library name: Brain-slides-HD01_2


title: F Ctrl 1

description: Library name: 1_S10

value: Female


title: GP

description: Library name: sample 1

value: bone cells

value: osteocytes


title: Brain-slides-HD01_n1

description: Library name: Brain-slides-HD01_1


title: m6A-WT-Input

value: spleen


title: Brain-slides-CCM01_n3

description: Library name: Brain-slides-CCM01_3

source_name: iPSCs CCM1_01

value: iPSCs CCM1_01

value: KRIT1 mutant


title: FTO-WT-RNA-seq-1

value: FTO-WT


title: Micorwell-seq datasets of patient5_replicate2

city: Hangzhou

first: Lifeng

last: Ma

address: Yuhangtang Road No.388

institute: Zhejiang University

data_processing:
Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-2.5.1. The reads quality under 10 were removed. We took a dark reaction for R1, where R1 measured 24bp and R2 measured 150bp. The cell barcode is at position 1-18 of R1, and the UMI barcode is at position 19-24 of R1.
scRNA-seq reads were aligned to the GRCh38 genome assembly using STAR (version 2.5.2a) with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix (DGE) based on UMI counts. The cell barcode is tagged with XC, the UMI is tagged with XM, and the gene is tagged with GE.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files of digital expression matrix (DGE) based on raw UMI counts, with genes as rows and cells as columns.

source_name: Breast

extract_protocol:
Tissues single-cell dissociation and lysate
Library preparations were performed with the Microwell-seq protocol

value: Breast

value: Inflammation


title: Brain-slides-CCM01_n1

description: Library name: Brain-slides-CCM01_1


title: Micorwell-seq datasets of patient5_replicate1


title: iECs-HD01_n2

description: Library name: iECs-HD01_2


title: m6A-KO-Input

value: FTO-KO


title: iECs-HD01_n3

description: Library name: iECs-HD01_3


title: iECs-HD01_n1

description: Library name: iECs-HD01_1


title: Brain endothelial cells harvested from intracranially injected GL261 tumor cells in Rab27a/b double hetrozygous mice

city: Montreal

first: Janusz

last: Rak

state: Quebec

address: 1001 Decarie Blvd. Room E01.4366

department: Department of Pediatrics

country: Canada

institute: McGill University

description:
10x Genomics 3 CellPlex Multiplexing single cell
JRak_Rab27_10x_cellranger_out.tar.gz
seurat_Lata_unfil.rds.tar.gz; seurat_Lata_fil.rds.tar.gz; seurat_Lata_endo_fil.rds.tar.gz

data_processing:
We used Cell Ranger v7.1.0 (10x Genomics) to demultiplex the raw sequencing reads to FASTQ files and align the reads to mouse reference mm10 to quantify gene counts
The gene count data has been processed following the Seurat pipeline, and low quality cells were filtered out by the following criteria: RNA less than 3000 counts, genes less than 500, mitochondrial gene fraction over 50% or 0
Doublets were removed out based on co-expression of different canonical marker sets. Endothelial cluster was separately analyzed and characterized based on previous studies on murine endothelial cells
Assembly: mm10
Supplementary files format and content: Gene count matrix by CallRanger and Seurat objects in .rds format including both unfiltered and filtered versions.

growth_protocol: The cells were freshly isolated from mouse brains. Therefiore, cells were not grown.

extract_protocol:
Brain tissues were dissociated and isolated using Collagenase/Dispase, debris separation using percoll and resuspended in PBS for single-cell capture.
Following the Chromium Single Cell 3’ Reagent Kits v3 User Guide, a single-cell RNA library was generated using the GemCode Single-Cell Instrument

treatment_protocol: The endothelial cells were isolated from the brains of mice which were either control (BEC) or injected intracranially with GL261 murine gliioma cell line (TEC) from Rab27a/b dHET and Rab27a/b dKO.

value: Brain

value: Murine glioma cell line

value: Rab27a/b dHET


title: iECs-CCM03_n3

description: Library name: iECs-CCM03_3

source_name: iPSCs CCM1_03

value: iPSCs CCM1_03


title: Micorwell-seq datasets of patient4_replicate3


title: Brain endothelial cells harvested from the brains of Rab27a/b double hetrozygous mice


title: m6A-KO-IP


title: iECs-CCM02_n1

description: Library name: iECs-CCM02_1

source_name: iPSCs CCM1_02

value: iPSCs CCM1_02

value: iPSCs-derived endothelial cells


title: iECs-CCM03_n2

description: Library name: iECs-CCM03_2


title: Micorwell-seq datasets of patient4_replicate2

value: Normal


title: Brain endothelial cells harvested from the brains of Rab27a/b double knockout mice

value: Rab27a/b dKO


title: iECs-CCM02_n3

description: Library name: iECs-CCM02_3


title: iECs-CCM02_n2

description: Library name: iECs-CCM02_2


title: Brain endothelial cells harvested from intracranially injected GL261 tumor cells in Rab27a/b double knockout mice


title: iECs-CCM03_n1

description: Library name: iECs-CCM03_1


title: iECs-CCM01_n2

description: Library name: iECs-CCM01_2


title: Micorwell-seq datasets of patient4_replicate4


title: Micorwell-seq datasets of patient3_replicate3


title: iECs-CCM01_n3

description: Library name: iECs-CCM01_3


title: iECs-CCM01_n1

description: Library name: iECs-CCM01_1


title: Brain-slides-CCM01_n2

description: Library name: Brain-slides-CCM01_2


title: Micorwell-seq datasets of patient3_replicate2