title: BioE-1197, rep3

city: Boston

first: Alberto

middle: Marin

last: González

state: MA

address: 3 Blackfan St

department: PCMM

institute: Boston Children's Hospital

data_processing:
bcl2fastq, standard parameters
bowtie2, -q --local -X 1000
samtools fixmate, sort, markdup
samtools index
bamCoverage (deeptools), --binSize 10 --normalizeUsing RPKM
Assembly: mm9
Supplementary files format and content: bigwig files normalized by RPKM and averaged using a running window of 10 bp

source_name: Spleen/lymph node

extract_protocol:
Nuclei were harvested by sequential lysis in lysis buffer one (LB1), two (LB2), and three (LB3) which were supplemented with protease inhibitor (ThermoFisher Scientfic Cat# 78429; 1X final concentration added right before use). LB1 consists of 50mM HEPES-KOH (pH 7.5, MilliporeSigma Cat# H4034 & P9333), 140mM NaCl (MilliporeSigma Cat# 7653), 1mM EDTA (pH 8.0, MilliporeSigma Cat# E6758), 10% glycerol (MilliporeSigma Cat# G5516), 0.5% Igepal CA-630 (MilliporeSigma Cat# I8896), 0.25% Triton X-100 (MilliporeSigma Cat# T8787) and KOH to adjust pH to 7.5. LB2 consists of 10mM Tri-HCl pH 8.0 (Quality Biological Cat# 351-007-101), 200 mM NaCl, 1mM EDTA pH 8.0, 0.5 mM EGTA and HCl to adjust pH to 8.0. LB3 consists of 10mM Tris-HCl (pH 8.0), 100 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 0.1% Sodium deoxycholate (MilliporeSigma Cat# 30970), 0.5% N-lauroylsarcosine (MilliporeSigma Cat# L7414) and HCl to adjust pH to 8.0. Cells were re-suspended in LB1 and rotated for 10 minutes at four degrees Celsius. Then, cells were pelleted at 2000 rpm, re-suspended in LB2 and rotated for 5 minutes at four degrees Celsius. Then, cells were pelleted at 2000 rpm and re-suspended in LB3. Nuclei were then sonicated at 4 degrees Celsius using a Fisher 150E Sonic Dismembrator with settings: 50% amplitude, 30 s ON, 30 s OFF for 12 min total time. Following sonication, samples were pelleted to remove cellular debris at 20,000g for 10 minutes at four degrees. After IP, DNA was extracted from reverse crosslinked chromatin samples by incubation with RNaseA (Thermo Fisher Scientific Cat# EN0531) for 15 min at 37C; and proteinase K (Thermo Fisher Scientific Cat# AM2546) for 1h at 65C. DNA was subsequently purified using MinElute (Qiagen Cat# 28004) purification.
DNA libraries were prepared and amplified using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs Cat# E7103L) and dual-indexed NEBNext Multiplex Oligos for Illumina (New England BioLabs Cat# E6440S). Final libraries were pooled, quantified with QuBit (Thermo), Bioanalyzer (Agilent) and qPCR (BioRad), then sequenced on a Novoseq SP 100 flow cell (Illumina) using paired-end 2x50bp

value: Spleen/lymph node

value: Primary

value: CD8+ OT-1 T cell


title: O3 TAM-3

status: Public on Sep 12 2023

type: SRA

city: Charlestown

first: Mei

last: Huang

address: Building 149 13th Street

country: USA

institute: Massachusetts General Hospital

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: tissue

value: tumor

tag: cell type

value: macrphages sorted from tumors

tag: genotype

tag: treatment

value: DMSO exposure


title: BioE-1197, rep2

library_source: genomic

molecule: genomic DNA

tag: cell line


title: Control, rep1

value: Control


title: Purkinje_cells_3

city: New York

first: Akshay

last: Shekhar

state: NY

address: 564 1st Ave Apt 11S

department: Medicine - Cardiology

institute: NYU School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8.4
Calculating insert size and standard deviation performed using Picard v.1.126
Reads were mapped using the STAR aligner (v2.5.0c)
read counting performed using HT-seq v0.6.0
Normalization and Deferential expression analysis performed using DEseq2 v3.0
BAM to bedgraph performed using bedtools v2.17.0
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.1.1
Assembly: mm10
Supplementary files format and content: BigWig

molecule: polyA RNA

source_name: Heart

extract_protocol: Cells were harvested and total RNAs were extracted using the RNeasy kit (Qiagen) according to the manufacture's protocol. Sequencing libraries were prepared using the TruSeq RNALibrary Prep Kit v2 (Illumina) according to the manufacture's protocol.

value: Heart

value: Cardiac Purkinje Cells

value: Wild Type


title: BioE-1197, rep1


title: sample 8944, patient 7 post-treatment biopsy, scRNA-seq

city: Geneva

first: Eliana

last: Marinari

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger Software v2.0.1/v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: matrix files and tab-separated values files

organism: Homo sapiens

source_name: brain

extract_protocol:
Before running single cell sequencing on brain samples, brain dissociation tissues were enriched using the EasySepTM Release Human CD45 Positive Selection Kit (Stemcell#100-0105). CD45 positive cells fraction were resuspended in 1× PBS with 0.04% bovine serum albumin. Cell numbers and viability were measured using a Countess II Automated Cell Counter (Thermo Fisher Scientific) as well as classical hemocytometer and trypan blue. Before running single cell on blood samples, PBMCs were enriched using the EasySep™ Human T Cell Enrichment Kit StemCell #19051. CD3 positive cells fraction were resuspended in 1× PBS with 0.04% bovine serum albumin. Cell numbers and viability were measured using a Countess II Automated Cell Counter (Thermo Fisher Scientific) as well as classical hemocytometer and trypan blue.
Library was performed according to manufacturer instructions (Single Cell 5', 10x Genomics protocol and Single Cell V(D)J for TCR sequencing).Single-cell suspensions were loaded onto a Chromium Single Cell Chip (5’ RNAseq Chromium Single Cell 5' Reagent Kit v2 Chemistry Dual Index, 10X Genomics) according to the manufacturer’s instructions for co-encapsulation with barcoded gel beads at a target capture rate of 10,000 individual cells per sample, based on the initial number of cells per sample. For all patients, RNA and TCR libraries were synthetized by following the Chromium Single Cell 5′ V(D)J Enrichment Kit, Human T Cell (10X Genomics, Chromium Single Cell Human TCR Amplification Kit)

value: brain

value: immune

tag: time

value: post-treatment

value: CART-EGFRvIII +Pembro

tag: individual

value: patient 7


title: WT221

city: Baltimore

first: Michael

middle: J.

last: Wolfgang

state: MD

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

description:
gene_count.txt
gene_fpkm.txt
TotalNormCounts041123v2.txt
Rab30KOvsRab30WT_deg.txt

data_processing:
Raw reads were filtered to remove reads containing adapters or reads of low quality.
Clean reads were mapped to the reference genome (GRCm38/mm10) using the HISAT2 software.
Gene counts were extracted and gene expression levels were estimated by the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM).
Pairwise comparisons of differential gene expression analysis was performed by read count normalization, model dependent p-value estimation, and FDR value estimation based on multiple hypothesis testing by Novogene's standard procedures.
Downstream analysis using the DESeq2 package in R was performed independently by the investigators to normalize raw read counts for comparisons across all samples.
Assembly: GRCm38/mm10
Supplementary files format and content: gene_count.txt includes raw readcount list with the annotation of each gene for each sample. Tab-delimited text file.
Supplementary files format and content: gene_fpkm.txt includes the FPKM list with the annotation of each gene for each sample.Tab-delimited text file.
Supplementary files format and content: TotalNormCounts041123v2.txt includes the downstream DESeq2 analysis (with Wald test, betaPrior=FALSE, and genes with at least 1 count) performed by the investigators with normalized read counts and the annotation of each gene for each sample.Tab-delimited text file.
Supplementary files format and content: Rab30_AlbCrevsRab30Cpt2_f_deg.txt includes the differential analysis results of all genes when comparing Rab30 liver-specific KO samples to Rab30;Cpt2 floxed control (littermates to DKO) samples. Tab-delimited text file.
Supplementary files format and content: Rab30KOvsRab30WT_deg.txt includes the differential analysis results of all genes when comparing Rab30 whole-body KO to WT littermates to Rab30 whole-body KO. Tab-delimited text file.
Supplementary files format and content: R30C2_AlbCrevsCpt2_AlbCre_deg.txt includes the differential analysis results of all genes when comparing Rab30;Cpt2 liver-specific DKO to Cpt2 liver-specific KO. Tab-delimited text file.
Supplementary files format and content: Cpt2_AlbCrevsRab30Cpt2_f_deg.txt includes the differential analysis results of all genes when comparing Cpt2 liver-specific KO to Rab30;Cpt2 floxed control (littermates to DKO). Tab-delimited text file.
Supplementary files format and content: R30C2_AlbCrevsRab30Cpt2_f_deg.txt includes the differential analysis of all genes when comparing Rab30;Cpt2 liver-specific DKO to Rab30;Cpt2 flozed control (littermates to DKO). Tab-delimited text file.

source_name: liver

extract_protocol:
Total RNA was extracted from flash frozen liver tissue using TRIzol reagent (Invitrogen for Thermo Fisher Scientific, 15596026) with additional purification using RNeasy Mini Kit (Qiagen, 74106), as per manufacturers’ instructions. RNA quality was assessed by nanodrop and independently by Novogene Corporation Inc (https://en.novogene.com/services/research-services/transcriptome-sequencing/).
RNA libraries for RNA-seq were prepared by Novogene following Novogene's standard protocols.

value: liver

value: WT littermate to Rab30 whole-body KO

value: 24hr fast


title: ATAC-seq_SL-3

city: Munich

first: Chenglei

last: Tian

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Munich

data_processing:
Clean reads were mapAll ATAC-seq reads were first mapped to the mm10 genome. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. ped to the Mus musculus mm10 reference genome using Bowtie2 (population) or Hisat2 (a few cells).
Normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads.
To visualize the ATAC-seq signal in the UCSC genome browser, we extended each read by 250 bp and counted the coverage for each base. The ATAC-seq enrichment was then summed within each 3-kb-window for the entire genome and was compared across different samples.
Pearson correlation was used for all analyses. All the ATAC-seq peaks were called by MACS with the parameters nolambda-nomodel. ATAC-seq peaks that are at least 2.5 kb away from annotated promoters (RefSeq, Ensemble and UCSC Known Gene databases combined) were selected as distal ATAC-seq peaks.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
Cells (500 to 3000 cells per reaction) were centrifuged to remove the supernatant. 20 μl of lysis buffer (10 mM Tris HCl (pH 7.4), 5 mM MgCl2, 10% DMF, 0.2% N-P40) was added, followed by pipetting 6-10 times to release the nuclei without purification, and 30 μl reaction buffer (10 mM Tris HCl (pH 7.4), 5 mM MgCl2, 10% DMF, 1000 unit Tn5) was mixed on a Vortex for 5 seconds. The reaction was incubated at 37 °C for 20 minutes, followed by addition of 350 μl ERC buffer (MiniElute, Qiagen) to stop the reaction. After DNA purification (MiniElute, Qiagen) and then performing ATAC-seq libraries construction.
Sequencing libraries were generated using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: SL: KO-DMEM medium+15%FBS+1000 IU mLIF, with Feeder; 2iL: N2B27 medium+1000 IU mLIF+3 μM Chir99021+1 μM PD0325901, with feeder; a2iL: N2B27 medium+1000 IU mLIF+3 μM Chir99021+1.5 μM CGP77675, with feeder; LCDM: N2B27 medium+1000 IU mLIF+3 μM Chir99021+2 μM Dim+ 2 μM Mih, with feeder; 2iL-F: N2B27 medium+1000 IU mLIF+3 μM Chir99021+1 μM PD0325901, without feeder.

tag: strain

value: Embryonic stem cell line


title: Purkinje_cells_2


title: sample 8862, patient 7 pre-treatment biopsy, scRNA-seq

description: 10x Genomics

value: pre-treatment


title: O3 TAM-2

value: tumor


title: O3 TAM-1

value: macrphages sorted from tumors


title: WT281


title: sample 8986, patient 6 post-treatment biopsy, scRNA-seq

description: 10x Genomics

value: patient 6


title: ExVivoTissue_MCT-treatedRat_28d_rap3

type: RNA

city: Beijing

first: Tiantai

last: Zhang

state: Beijing

address: No. 1, Xiannongtan Street

department: Institute of Materia Medica

country: China

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

description: Gene expression of rat lung tissue after 4w by one dose of MCT intaperitonel injection.

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

organism: Rattus norvegicus

source_name: Lung tissue, MCT rat, 28d, raplicate3

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.The purity and concentration of total RNA samples were determined with NanoDrop ND-1000.

treatment_protocol: Rats were treated by one dose of MCT(60mg/kg,Intraperitoneal injection) or saline, and control rats were injected with the equivalent volume of dissolvent solution according to their weights. Freshly lung tissues were isolated from rats after 28d and  perfusion with PBS.

value: Lung tissue

tag: gender

value: male

tag: age


title: O3 TAM-5

value: DMSO exposure


title: WT952


title: ExVivoTissue_MCT-treatedRat_28d_rap2

source_name: Lung tissue, MCT rat, 28d, raplicate2


title: WT951


title: sample 8742, patient 6 pre-treatment biopsy, scRNA-seq

description: 10x Genomics


title: A3 TAM-5

value: DMBA exposure


title: sample 8945, patient 5 post-treatment biopsy, scRNA-seq

description: 10x Genomics

value: brain

value: patient 5


title: KO4

value: Rab30 whole-body KO


title: A3 TAM-4


title: sample 8761, patient 2 post-treatment blood, scRNA-seq

description: 10x Genomics

source_name: blood

value: blood

value: immune

value: post-treatment

value: CART-EGFRvIII +Pembro

value: patient 2


title: KO3

value: liver

value: 24hr fast


title: A3 TAM-3

value: tumor


title: ExVivoTissue_Saline-treatedRat_28d_rap3

description: Gene expression of rat lung tissue after 4w by one dose of saline intaperitonel injection.

source_name: Lung tissue, normal rat, 28d, raplicate3


title: KO2


title: ExVivoTissue_Saline-treatedRat_28d_rap2

source_name: Lung tissue, normal rat, 28d, raplicate2


title: sample 8688, patient 4 post-treatment blood, scRNA-seq

description: 10x Genomics

value: patient 4


title: A3 TAM-2

value: macrphages sorted from tumors


title: Sufu-cKO5

city: Shanghai

first: jiayin

last: Peng

address: Yueyang Road

institute: Center for Excellence in Molecular Cell Science

data_processing:
The image data measured by the high- throughput sequencer are converted into sequence data ( reads) by CASAVA base recognition. Raw data ( raw reads) of fastq format were firstly processed through in- house perl scripts. In this step, clean data ( clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non- splice mapping tools.
Supplementary files format and content: all_compare file includes raw counts, FPKM for each sample

source_name: Peritoneal exudate macrophages

growth_protocol: PEM were isolated from WT and Sufu-cKO mice. Isolated PEMs were seeded and cultured at 37℃, 5% CO2 for 48 h.

extract_protocol:
Cells were collected directly into TRIzol and RNA was extracted using a QIAGEN RNeasy Mini Kit according to the manufacturer’s instructions. The integrity of the isolated RNA was verified using a Bioanalyzer (Agilent 2100).
10 ng of high-quality RNA (RNA integrity number, RIN> 8) was used to produce cDNA libraries using the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme) according to the manufacturer’s instructions and sequenced on an Illumina NextSeq sequencer.

treatment_protocol: Then, cells were treated with LPS for 3 h, respectively.

value: Peritoneal exudate macrophages

value: Macrophage

value: Lyz-cre;Sufu(f/f)

value: LPS 3h


title: ExVivoTissue_MCT-treatedRat_28d_rap1

source_name: Lung tissue, MCT rat, 28d, raplicate1

value: Lung tissue

value: male


title: KO1

value: Rab30 whole-body KO


title: sample 8688, patient 4 post-treatment biopsy, scRNA-seq

description: 10x Genomics

value: brain


title: sample 8510, patient 1 post-treatment blood, scRNA-seq

description: 10x Genomics

value: blood

value: immune

value: patient 1


title: A3 TAM-6

value: DMBA exposure


title: sample 8510, patient 1 post-treatment biopsy, scRNA-seq

description: 10x Genomics

value: post-treatment

value: CART-EGFRvIII +Pembro


title: EnVivoTissue_HypoxicRat_21d_rap1

description: Gene expression of rat lung tissue after hypoxia-treated for 21d

source_name: Lung tissue, hypoxia, 21d, raplicate1

treatment_protocol: Rat were exposed normoxia or hypoxia (10% oxygen) for 21d, freshly lung tissues from rats were isolated and perfused with PBS.


title: Sufu-cKO3


title: Sufu-cKO4


title: EnVivoTissue_NormoxicRat_21d_rap2

description: Gene expression of rat lung tissue after normoxia-treated for 21d

source_name: Lung tissue, normoxia, 21d, raplicate2


title: EnVivoTissue_NormoxicRat_21d_rap3

source_name: Lung tissue, normoxia, 21d, raplicate3


title: EnVivoTissue_HypoxicRat_21d_rap3

source_name: Lung tissue, hypoxia, 21d, raplicate3


title: Sufu-cKO2


title: sample 8761, patient 2 post-treatment biopsy, scRNA-seq

description: 10x Genomics

value: patient 2


title: Sufu-cKO1


title: WT5

value: Sufu(f/f)


title: Organoid cells, TSHZ3 shRNA-treated and mCherry–, scRNAseq

city: Los Angeles

first: Patricia

last: Nano

state: CA

address: 615 Charles E Young Dr S

institute: University of California, Los Angeles

description: PIP-seq

data_processing:
FASTQ files were aligned to a custom reference containing the human genome (GRCh38), an mCherry sequence, and genomes of four common mycoplasma species using PIPseeker software, version 02.01.04 (Fluent Biosciences), sensitivity set to 3 according to default manufacturer recommendations. For each sample, count matrices were converted to Seurat objects using the Read10X function, Seurat version 4 (Stuart, PMID: 31178118). Samples were merged into one Seurat object, and the Seurat pipelines described above were used to perform rigorous quality control (omit genes detected in < 3 cells and cells with < 500 genes detected and/or > 5% of UMIs mapping to mitochondrial genes), and confirm the lack of mycoplasma infection in our dataset (< 1% of UMIs in the dataset post-QC mapping to mycoplasma genomes).  Using Seurat, we clustered cells based on their gene profiles, calculated and scored cluster markers, assigned cell type based on marker expression, and calculated UMAP coordinates.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files, matrix files, and comma-seprated values files

source_name: UCLA 1

growth_protocol: Human embryonic stem cells used for this study were between passage 12 – 24.

extract_protocol:
At week 8, organoids were processed for single-cell transcriptomics using the PIPseq™ T2 3’ Single Cell RNA Kit v4.0 (Fluent Biosciences). Cortical organoids were dissociated into single-cell suspensions via 30-min incubation at 37 ºC in papain and DNAse in EBSS (Cat. # LK003150, Worthington), shaking vigorously every 5-10 min. Samples were then triturated with manual pipetting 10 times, and pelleted with a 5 min spin at 300 g in 4 ºC. For hESC 1 (UCLA 6) samples, pellets were resuspended in the provided Cell Resuspension Buffer (Fluent Biosciences), and 5,000 cells were targeted for capture. For hESC 2 (UCLA 1) samples, pellets were resuspended in 2% FBS in PBS, then passed through a wet 35 µm cell strainer into round-bottom tubes for flow cytometry assisted cell sorting (FACS). Samples were treated with DAPI (1:1000) to identify dead cells, and processed on a FACSAria (BD Biosciences). FACS gates were set using uninfected cells, and mCherry– and mCherry+ sorted samples were pelleted once more and resuspended in 5 µL of 2% FBS in PBS. This process enabled the targeting of ~ 25,000 cells for capture, with the exception of mCherry+ cells from FEZF2 #1-shRNA-transduced organoids (7,500 cells targeted).
Sequencing libraries were obtained from cells according to PIPseq T2 instructions, using 16 – 17 cycles for cDNA amplification and 8 – 12 cycles for library amplification depending on the amount of DNA. Libraries were quantified on an Agilent 2100 Bioanalyzer, and and sequenced as per manufacturer recommendation on a NovaSeq S2 flow cell.

treatment_protocol: At the second passage post-thaw, cells were infected with lentiviral supernatants encoding shRNAs. One ~ 70% confluent six-well well of stem cells was passaged and expanded onto 4 – 6 six-well wells, each of which containing 5 µM Rock inhibitor, 10 µg/mL polybrene (Cat. # TR-1003-G, Millipore Sigma), and 1:200 lentivirus in mTesR+ media. Media was changed 18 hours after infection. All lines were maintained and expanded, undergoing a maximum of one passage between infection and organoid aggregation. Organoids generated based on protocols described in Kadoshima et al., 2013 (PMID: 24277810) and Bhaduri et al., 2020 (PMID: 31996853).

value: UCLA 1


title: Organoid cells, FEZF2 #2 shRNA-treated and mCherry–, scRNAseq

description: PIP-seq


title: A3 TAM-1

value: tumor

value: macrphages sorted from tumors


title: Organoid cells, TSHZ3 shRNA-treated and mCherry+, scRNAseq

description: PIP-seq


title: Organoid cells, FEZF2 #2 shRNA-treated and mCherry+, scRNAseq

description: PIP-seq


title: WT4

value: Peritoneal exudate macrophages

value: Macrophage


title: WT3

value: LPS 3h


title: WT2


title: EnVivoTissue_HypoxicRat_21d_rap2

source_name: Lung tissue, hypoxia, 21d, raplicate2

value: Lung tissue

value: male


title: DKO943

description:
gene_count.txt
gene_fpkm.txt
TotalNormCounts041123v2.txt
R30C2_AlbCrevsCpt2_AlbCre_deg.txt
R30C2_AlbCrevsRab30Cpt2_f_deg.txt

value: liver

value: Rab30;Cpt2 liver-specific DKO

value: 24hr fast


title: Organoid cells, FEZF2 #1 shRNA-treated and mCherry–, scRNAseq

description: PIP-seq


title: sample 8167, patient 1 pre-treatment biopsy, scRNA-seq

description: 10x Genomics

value: brain

value: immune

value: pre-treatment

value: patient 1


title: WT1


title: DKO232


title: ExVivoTissue_Saline-treatedRat_28d_rap1

source_name: Lung tissue, normal rat, 28d, raplicate1


title: Aged_15_mnth_mice_6_bulk_miRNAseq_hypothalamus

city: Bongmyeongdong

first: Mihye

last: Lee

state: Cheonan

address: 25, Bongjeong-ro, Dongnam-gu, Cheonan-si, 31151, Korea

department: Department of Integrated Biomedical Science

country: South Korea

institute: Soonchunhyang Institute of Medi-bio Science (SIMS)

data_processing:
Small RNA raw sequencing reads are filtered based on their quality.
The readings are aligned to the reference mouse genome (mm10) and miRBase v21 precursor miRNAs to find known and novel miRNAs.
The miRDeep2 algorithm is then used to predict potential hairpin structures.
Unique cluster reads are then sequentially matched against the reference mouse genome, miRBase v21, and the non-coding RNA database, Rfam9.1 to classify known miRNAs.
Read counts for each miRNA are extracted from mapped miRNAs to report the abundance of each miRNA.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Aged male C57BL/6J mice

extract_protocol:
The total RNA of the samples was extracted with the Trizol (Invitrogen) reagent and used for construction of sequencing libraries.
miRNA libraries for miRNA-seq were prepared using TruSeq Small RNA Library Prep Kit following manufacturer's protocols.

value: Hypothalamus

tag: Sex

value: 15 months


title: Aged_15_mnth_mice_5_bulk_miRNAseq_hypothalamus


title: EnVivoTissue_NormoxicRat_21d_rap1

source_name: Lung tissue, normoxia, 21d, raplicate1


title: Organoid cells, TSHZ3 shRNA, scRNAseq

description: PIP-seq

source_name: UCLA 6

value: UCLA 6


title: Organoid cells, scram shRNA-treated and mCherry+, scRNAseq

description: PIP-seq

value: UCLA 1


title: DKO233

source_name: liver


title: Rab30cff980

description:
gene_count.txt
gene_fpkm.txt
TotalNormCounts041123v2.txt
Rab30_AlbCrevsRab30Cpt2_f_deg.txt

value: Rab30 liver-specific KO


title: Organoid cells, FEZF2 shRNA #2, scRNAseq

description: PIP-seq


title: Young_2_mnth_mice_3_bulk_miRNAseq_hypothalamus

source_name: Young male C57BL/6J mice

value: 2 months


title: Rab30cff978


title: Organoid cells, scram shRNA-treated and mCherry–, scRNAseq

description: PIP-seq


title: Young_2_mnth_mice_2_bulk_miRNAseq_hypothalamus


title: Organoid cells, scram shRNA, scRNAseq

description: PIP-seq


title: Rab30cff741


title: Organoid cells, FEZF2 shRNA #1, scRNAseq

description: PIP-seq


title: DKO247


title: Organoid cells, FEZF2 #1 shRNA-treated and mCherry+, scRNAseq

description: PIP-seq


title: Rab30cff979


title: Aged_15_mnth_mice_6_bulk_miRNAseq_hippocampus

source_name: Aged male C57BL/6J  mice

value: Hippocampus


title: Apold1 KO_16h_angoigenic_03

city: Zürich

first: Lukas

middle: Matthias

last: von Ziegler

address: Winterthurerstrasse 190

department: D-HESZ

institute: ETH Zürich

data_processing:
Pseudoalignment using kallisto (version 0.44.0) on the GENCODE M17 transcriptome
Aggregation on the protein coding level
Assembly: GRCm38
Supplementary files format and content: .tar.gz zipped directories with kallisto output (pseudoaligned read counts and tpm measures of trancripts) containing .h5 and .tsv files

source_name: Hind leg muscle

extract_protocol:
Trizol
illumina TrueSeq

value: Hind leg muscle

tag: replicate

value: biol rep 3

value: FACS sorted smooth muscle Ecs

value: endothelial cells

value: Apold1 KO

tag: protocol

value: 16h angoigenic medium incubation


title: primary Delta gene expression library

city: Tucson

first: Deepta

last: Bhattacharya

state: AZ

address: 1656 E Mabel St

department: Immunobiology

institute: University of Arizona

description:
RC048, RC079, RC214, RC182, RC156, RC242, RC113, RC281, RC362, RC396
pd.barcodes.tsv.gz
pd.matrix.mtx.gz
pd.features.tsv.gz

data_processing:
the demultiplexing, barcoded processing, gene counting and -multi were made using cell ranger (https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/tutorial/tutorial-multi)
data were analyzed using Seurat v4.1.3
Supplementary files format and content: tab-separated values and matrix files

source_name: pbmc

extract_protocol:
GEM generation and RT
Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) User Guide with Feature Barcode technology for Cell Surface Protein & Immune Receptor Mapping

value: pbmc


title: wild type_16h_angoigenic_03

value: wild type

value: male


title: Young_2_mnth_mice_1_bulk_miRNAseq_hypothalamus


title: Aged_15_mnth_mice_4_bulk_miRNAseq_hypothalamus


title: primary Delta immune profiling library

description:
HTO_C0251 - RC048, HTO_C0252 - RC079, HTO_C0253 -RC214, HTO_C0254 - RC182, HTO_C0255 - RC156, HTO_C0256 - RC242, HTO_C0257 - RC113, HTO_C0258 - RC281, HTO_C0259 - RC362, HTO_C0260 - RC396; ADT_C0951 - WT-S1, ADT_C0952 - Delta-S1, ADT_C0953 - Delta NTD + WT-S1, ADT_C0954 - Delta RBD/L452, ADT_C0955 - Delta RBD
pd.barcodes.tsv.gz
pd.matrix.mtx.gz
pd.features.tsv.gz

library_source: other

molecule: other


title: Aged_15_mnth_mice_5_bulk_miRNAseq_hippocampus


title: wild type_16h_angoigenic_02

value: biol rep 2


title: Aged_15_mnth_mice_4_bulk_miRNAseq_hippocampus


title: post-vaccination Delta gene expression library

description:
RC095, RC019, RC018, RC121, RRC097, RC066, RC134, RC012, RC061, RC056
bt.barcodes.tsv.gz
bt.matrix.mtx.gz
bt.features.tsv.gz


title: Apold1 KO_16h_angoigenic_02


title: post-vaccination Delta vdj library

description:
HTO_C0251 - RC095, HTO_C0252 - RC019, HTO_C0253 -RC018, HTO_C0254 - RC121, HTO_C0255 - RC097, HTO_C0256 - RC066, HTO_C0257 - RC134, HTO_C0258 - RC012, HTO_C0259 - RC061, HTO_C0260 - RC056; ADT_C0951 - WT-S1, ADT_C0952 - Delta-S1, ADT_C0953 - Delta NTD + WT-S1, ADT_C0954 - Delta RBD/L452, ADT_C0955 - Delta RBD
bt.barcodes.tsv.gz
bt.matrix.mtx.gz
bt.features.tsv.gz


title: Young_2_mnth_mice_2_bulk_miRNAseq_hippocampus


title: Young_2_mnth_mice_3_bulk_miRNAseq_hippocampus


title: Apold1 KO_16h_angoigenic_01

value: biol rep 1


title: post-vaccination Delta immune profiling library

description:
bt.barcodes.tsv.gz
bt.matrix.mtx.gz
bt.features.tsv.gz


title: wild type_16h_angoigenic_01


title: MV4-IgG

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

data_processing:
Raw data of CUT-TAG was aligned to the reference genome (UCSC hg38) using Bowtie2 (v 2.4.4)
Peaks were identified using MACS3 (v3.0)
Assembly: hg38
Supplementary files format and content: peak text files
Library strategy: CUT &TAG

extract_protocol:
HyperactiveUniversalCUT&TagAssayKitfor Illumina (Vazyme #TD903)
HyperactiveUniversalCUT&TagAssayKitfor Illumina (Vazyme #TD903)

tag: chip antibody

value: IgG

value: untreated


title: Apold1 KO_None_04

value: no incubation


title: Young_2_mnth_mice_1_bulk_miRNAseq_hippocampus


title: MV4-NC


title: Apold1 KO_None_05

value: biol rep 4


title: macrophage_5ng_GM-CSF-3

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Reads were aligned to mouse genome (mm10) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against RefSeq gene annotation
Gene expression level from RNA-Seq is measured by rpkm (PMID: 18516045) with an in-house script.
Assembly: mm10
Supplementary files format and content: First colum: entrz ID; second column: gene symbol; columns thereafter: log2(RPKM+1)+0.0001 for each sample.

source_name: PyMT murine breast tumor

extract_protocol:
RNA from the sorted TAMs and CD8 + T cells was isolated using RNeasy Plus Mini Kit (Qiagen 74136) and further concentrated using RNeasy MinElute Cleanup Kit (Qiagen 74204). Library preparation and sequencing were performed at the Genomics Core Facility of West Virginia University and  Marshall University, respectively.
When building these libraries we started with RNA that was too low to quantify as it was extracted from a small number of cells. THe libraries were built with NEB's Low Input mRNA prep and Illumina compatible UDI's (also from NEB) following manufacturers suggested protocol. Generate cDNA with 21 cycles. After cDNA synthesis/amplification, bring 10ng amplifies cDNA into the fragmentation/end prep step.   Use 8 cycles PCR for final amplification.

value: 5ng GM-CSF

tag: tissue/cell type

value: macrophage

value: FVB/NJ


title: Apold1 KO_None_03

value: Hind leg muscle

value: biol rep 3


title: MV4-shANP32B

value: ANP32B knockdown


title: macrophage_5ng_GM-CSF-2


title: macrophage_5ng_GM-CSF-1


title: macrophage_Saline-3

value: Saline


title: Apold1 KO_None_01

value: FACS sorted smooth muscle Ecs

value: endothelial cells

value: Apold1 KO


title: Kasumi-IgG

source_name: Kasumi-IgG

value: Kasumi


title: macrophage_Saline-2


title: Kasumi-shANP32B


title: Kasumi-NC

source_name: Kasumi-NC


title: wild type_None_05

value: biol rep 5

value: wild type

value: male


title: macrophage_Saline-1


title: Dynabeads activated

first: Youcheng

last: Yang

state: California

address: 430 Westwood Plaza, 5121 Engineering V, Box 951600, Attn (PI NAME): Li Lab

department: Bioengineering

institute: UCLA

data_processing:
Rstudio Build 353
Remove cells with extreme mitochondria counts, RNA counts, or RNA features, then normalize the data
Select features that are repeatedly variable across datasets for integration and perform integration
Perform linear dimensional reduction using PCA
Cluster the cells and run non-linear dimensional reduction using UMAP
Assembly: GRCh38
Supplementary files format and content: HDF5 files with the feature-barcode matrix
Supplementary files format and content: The files are the filtered version that contains only detected cellular barcodes.

source_name: Peripheral blood mononuclear cells

extract_protocol:
Performed by UCLA Technology Center for Genomics and Bioinformatics
Library preparation was accomplished using the Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)

treatment_protocol: On day 0, healthy donor PBMCs were activated by SynVACs or Dynabeads  relatively. An initial number of 5 x 105 PBMCs were seeded in the starting culture media supplied with 30 IU/ml recombinant IL-2 and activated by SynVACs, or Dynabeads at a bead-to-cell ratio of 1:1. On day 2, cells were transduced with Lenti/CAR19 or Lenti/MCAR virus for another 24 hours. The resulting CAR-T cells were expanded for another 12 days in C10 medium, fresh media supplied with 30 IU/ml recombinant IL-2 was supplemented if needed, and then the generated CAR-T cells were collected for sequencing at day 14.

value: Peripheral blood mononuclear cells

value: Sorted with with a FACSAria II flow cytometer for pure T cells


title: pure line of C. gibelio, infected group, repl. 5

city: Brno

first: Jiri

last: Vorel

address: Kotlarska 267/2

department: Department of Botany and Zoology

country: Czech Republic

institute: Masaryk University

description: gibel.featureCounts.tsv

data_processing:
Quality check (FastQC v. 0.11.9)
Quality trimming (Trimmomatic v. 0.36, CROP:250 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:35)
Alignment (STAR v. 2.7.3a; employing default parameters, except for --outFilterMismatchNoverLmax 0.1 and --twopassMode Basic)
Quality control after alignment concerning the number and percentage of uniquely- and multi-mapped reads, rRNA contamination, the mapped regions, the read coverage distribution, strand specificity, gene biotypes, and PCR duplication was performed using several tools (RSeQC v. 2.6.2; Picard toolkit v. 2.18.27; Qualimap v. 2.2.2; BioBloom tools v. 2.3.4)
DGE analysis (featureCounts v. 1.6.3 with settings -s 2 -T 10 -F GTF -Q 0 -d 1 -D 25000; DESeq2 v1.20.0)
Functional annotation (KEGG pathway database; clusterProfiler v 3.12.0)
Assembly: ASM336829v1, GCA_000951615.2
Supplementary files format and content: tab-delimited text file with featureCounts for samples that originated and mapped significantly better on the C. carpio reference genome
Supplementary files format and content: tab-delimited text file with featureCounts for samples that originated and mapped significantly better on the C. gibelio reference genome

organism: Carassius gibelio

source_name: Head kidney

growth_protocol: Catching and artificial breeding

extract_protocol:
NEBNext Poly(A) mRNA Magnetic Isolation Module
NEBNext Ultra Directional RNA Library Prep Kit for Illumina

value: Head kidney


title: pure line of C. gibelio, infected group, repl. 4

description: gibel.featureCounts.tsv


title: pure line of C. gibelio, infected group, repl. 3

description: gibel.featureCounts.tsv


title: wild type_None_04

value: biol rep 4

value: no incubation


title: pure line of C. gibelio, infected group, repl. 2

description: gibel.featureCounts.tsv


title: wild type_None_03


title: CD8-T-cells_5ng_GM-CSF-2

value: 5ng GM-CSF

value: CD8 T cells

value: FVB/NJ


title: pure line of C. gibelio, infected group, repl. 1

description: gibel.featureCounts.tsv


title: U3121,glioblastoma, cells [SMAD3_U3121 Cut&Run]

city: Umeå

first: Silvia

last: Remeseiro

state: Västerbotten

address: UNIVERSITETSTORGET 4

department: UCMM

country: Sweden

institute: Umeå University

data_processing:
library strategy: Cut and Run
Raw reads were mapped to the human genome (hg38, Ensembl genome version 96, ensembl.org) using bowtie2 (options: -f BAMPE --threads 4 --very-sensitive).
Enriched peaks were called using MACS2 (options: -f BAMPE --broad -g hs -B -q 0.05).
Peaks were called on the target data at 1% of regions with enriched signals using SEACR with the following parameters: 0.01 norm stringent
Assembly: hg38
Supplementary files format and content: bed files

growth_protocol:
Astrocytes were cultured in AGM, or Astrocyte Growth Medium (#CC-3186) in humidified atmosphere with 5% CO2 at 37C
GBM Cells were grown in Feed Medium, which is composed of DMEM/F12 Glutamax (GIBCO, Life Technologies) and Neurobasal medium (GIBCO) mixed in 1:1 ratio, containing 1X B27 (Invitrogen, Life Technologies), 1X N2 (Invitrogen, Life Technologies), 1% penicillin/streptomycin (Sigma-Aldrich)), and supplemented with the growth factors endothelial growth factor (EGF) (10 ng/ml) and fibroblast growth factor (FGF) (10 ng/ml) (PeproTech, EC Ltd).
OPCs (Creative Biolabs CAT#: NCL-2103-P49) were cultured in Oligodendrocyte Precursor Cell Growth Medium [CAT#: NCL-21P6-106] in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Approximately 100 thousend cells were cross-linked with 0.1% formaldehyde for 2 minutes
After quenching and cell lysis, CUT&RUN Assay kit (#86652, Cell Signaling Technologies) instructions were followed and  IP was done with either 1.2ug of  SMAD3 (Abcam #ab208182), or 4ug of PITX1 (Santa Cruz, #sc-271435 X)
Libraries were prepared using the DNA library Prep Kit for illumine(Cell Signaling Technologies #56795).

value: mesenchymal

value: WT


title: CD8-T-cells_5ng_GM-CSF-1


title: U3118,glioblastoma, cells [SMAD3_U3118 Cut&Run]

value: proneural


title: Apold1 KO_None_02

value: Hind leg muscle

value: biol rep 2

value: FACS sorted smooth muscle Ecs

value: endothelial cells


title: wild type_None_02

value: wild type


title: pure line of C. gibelio, control group, repl. 2

description: gibel.featureCounts.tsv


title: pure line of C. gibelio, control group, repl. 3

description: gibel.featureCounts.tsv


title: wild type_None_01

value: biol rep 1

value: male


title: CD8-T-cells_Saline-1

value: Saline


title: U3086,glioblastoma, cells [SMAD3_U3086 Cut&Run]

value: classical


title: Wildtype SPC+ sorted Cells

city: Philadelphia

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the STARSolo 2.7.9a and downstream analysis performed using Seurat v4
Assembly: mm39

source_name: Lung

growth_protocol: ARIES protocol #806345

extract_protocol:
Target cells were FACS sorted and were loaded onto the 10x Chromium (10X Genomics) aiming for 10,000 cells per sample.
Libraries were prepared according to the manufacturer’s protocol using Chromium Single Cell 3’ v2 chemistry.

treatment_protocol: ARIES protocol #806345

value: Epithelial cells  Epithelial cells  Epithelial cells

value: Lung

value: Sftpc-creERT2; R26R_EYFP

value: 14 Day Post Flu

value: 8-10 weeks old


title: CD8-T-cells_Saline-2

value: CD8 T cells

value: FVB/NJ


title: U3085,glioblastoma, cells [SMAD3_U3085 Cut&Run]

value: neural

value: WT


title: pure line of C. gibelio, control group, repl. 1

description: gibel.featureCounts.tsv

value: Head kidney


title: CD8-T-cells_5ng_GM-CSF-3

value: 5ng GM-CSF


title: U3078,glioblastoma, cells [SMAD3_U3078 Cut&Run]

value: mesenchymal


title: Tfcp2l1 KO SPC+ sorted Cells

description: 10x Genomics

value: Sftpc-creERT2; Tfcp2l1 fl/fl; R26R_EYFP


title: SynVACs activated

value: Peripheral blood mononuclear cells

value: Sorted with with a FACSAria II flow cytometer for pure T cells


title: Tfcp2l1 KO Post Flu Sample 6

data_processing:
Fastq files were align to the mm39 reference genome using STAR and default parameters
Ensmebl v104 gene annotations were used for gene counts, gene counts were obtain using STAR
Raw gene counts were transformed using 'LIMMA-Voom' method and differential gene expression conducted using LIMMA.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include VOOM adjusted cpms values for each Sample

extract_protocol: none provided by the submitter

value: 14 day post flu


title: CD4T-FL-DLBCL-Tonsil-Run3-TCRseq

city: Oslo

first: Ivana

last: Spasevska

address: Disenveien 9

country: Norway

institute: University of Oslo

description: 10X Genomics

data_processing:
bcl2fastqv2.20 pipeline was used to demultiplex raw base-call files, convert them into FASTQ files
Cell Ranger3.0.2-count was used on default parameters to generate single cell feature counts for a single library
Single Cell V(D)J sequencing was analyzed using cellranger- 2.2.0 version.  Reference used:
The downstream analysis and integrationis performed using R programming Language and Seurat version 4
Assembly: refdata-cellranger-GRCh38-3.0.0(scRNASeq) &  V(D)J Reference GRCh38-alts-ensembl(VDJ seq)
Supplementary files format and content: Cell ranger count output: filtered count matrix, barcodes and features.
Supplementary files format and content: Filtered contig annotations

source_name: lymph nodes

extract_protocol:
Single-cell suspensions from FL (n = 3), DLBCL (n = 3) and tonsillar (n = 3) samples were thawed and depleted for B cells using CD19 pan-B dynabeads (ThermoFischer), following manufacturer’s instructions. Following B-cell depletion, cells were stained with 2 μM Fixable Viability Dye – Alexa 750 for 10 min at 4°C for live/dead cell discrimination. The samples were washed in PBS, stained with the same panel of fluorochrome-coupled antibodies and CITE-seq antibodies, and TotalSeq-C hashtag antibody,  prior to cell sorting. Live CD4+ T cells (Alexa750−CD3+CD4+CD8−) were then sorted on a FACS Aria. For single-sample processing, 13 000 cells from each sample (tonsil, FL and DLBCL) were sorted directly into the same tube of PBS with 0.05% BSA and subsequently spun down and reconstituted in 30 µl PBS with 0.05% BSA, to yield a total of 30,000 cells/30 µL.
Utilizing 10X Genomics Chromium Controller and Chromium Single Cell 5′ Gel Bead kit, approximately 20,000 cells per reaction (containing 3 hash-tagged samples) were partitioned into nanoliter droplets to achieve approximately 7-9,000 individual cells (2-3,000 per sample). All samples were loaded on the Chromium Controller within less than 30 min of cell sorting. The resulting barcoded cDNA was used to generate sequencing libraries for gene expression (Chromium Single Cell 5’ Library kit), for TCR analysis (Chromium Single Cell V(D)J Enrichment kit, Human T Cell) and antibody analysis (Chromium Single Cell 5’ Feature Barcode Library Kit), according to the manufacture’s protocols. All sequencing libraries were sequenced together on Illumina NextSeq500 according to manufacturer’s recommendations.

value: lymph nodes

value: CD4 T cells


title: T102 [HA_024]

city: Hanover

first: Hugo

last: Arias-Pulido

state: NH

address: 621 Rubin Building - HB 7936 1 Medical Center Drive

department: Department of Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

data_processing:
FastQC was used for quality control of raw sequences
Trimming of adapter sequences and poly-A tails was performed with cutadapt. Trimmed reads were aligned to the Canis lupus familiaris genome (RefSeq accession: GCF_000002285.5) using STAR.
Raw counts were generated for each gene using combat (v.3.42.0). Expression levels for each transcript were normalized using DESeq2's median of ratios. Differential gene expression analysis was conducted using the DESeq2 package.
Supplementary files format and content: comma separated value file includes counts for each sample
Assembly: canFam6

organism: Canis lupus familiaris

source_name: mammary carcinoma

extract_protocol:
Snap-frozen tumor samples were used for rna isolation. RNA was extracted using the Rneasy Mini Kit (Qiagen, Redwood City, CA) after homogenization by beating with 2mm stainless steel beads in Qiagen RLT buffer.
RNA-seq libraries were prepared using the Lexogen QuantSeq Rev kit following manufacturer's protocols and sequencing as single-end, 100bp reads on a NextSeq2000 instrument.

treatment_protocol: The largest tumor in each patient was the target tumor (injected) with eCPMV immunotherapy. In enrolled patients, a pretreatment incisional biopsy of the target injected tumor was taken before eCPMV immunotherapy, followed by intratumoral eCPMV injection immediately after obtaining the tumor biopsy sample. Two intratumoral doses of eCPMV immunotherapy were administered, the first on day 0 (D0) and the second between days six and nine (D6-D9; DTx2), followed by surgery on D12-D17 (DSx) at which time the injected tumor was resected and a surgical biopsy was collected for histopathology and research studies.

value: mammary carcinoma

value: nanoparticle


title: Tfcp2l1 KO Post Flu Sample 5

value: Lung


title: U3073,glioblastoma, cells [SMAD3_U3073 Cut&Run]


title: CD4T-FL-DLBCL-Tonsil-Run3-scRNAseq-CITEseq

description:
10X Genomics
TotalSeq-C0063 anti-human CD45RA Antibody,TotalSeq-C0085 anti-human CD25 Antibody, TotalSeq-C0088 anti-human CD279 (PD-1) Antibody, TotalSeq-C0089 anti-human TIGIT (VSTM3) Antibody, TotalSeq-C0144 anti-human CD185 (CXCR5) Antibody, TotalSeq-C0158 anti-human CD134 (OX40) Antibody, TotalSeq-C0171 anti-human/mouse/rat CD278 (ICOS) Antibody, TotalSeq-C0390 anti-human CD127 (IL-7Rα) Antibody
TotalSeq-C0251 anti-human Hashtag 1 Antibody, TotalSeq-C0252 anti-human Hashtag 2 Antibody, TotalSeq-C0253 anti-human Hashtag 3 Antibody


title: T101 [HA_023]


title: CD4T-FL-DLBCL-Tonsil-Run2-TCRseq

description: 10X Genomics


title: U3054,glioblastoma, cells [SMAD3_U3054 Cut&Run]


title: CD4T-FL-DLBCL-Tonsil-Run2-scRNAseq-CITEseq


title: CD4T-FL-DLBCL-Tonsil-Run1-TCRseq

description: 10X Genomics


title: Tfcp2l1 KO Post Flu Sample 4


title: T071 [HA_021]


title: T072 [HA_022]


title: Tfcp2l1 KO Post Flu Sample 3


title: U3031,glioblastoma, cells [SMAD3_U3031 Cut&Run]


title: T052 [HA_020]


title: Tfcp2l1 KO Post Flu Sample 2


title: U3028,glioblastoma, cells [SMAD3_U3028 Cut&Run]

value: classical


title: CD4T-FL-DLBCL-Tonsil-Run1-scRNAseq-CITEseq


title: RH30_DMSO_24h_r2_200108_T

city: Bethesda

first: Javed

last: Khan

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

description: control sample biological replicate 2

data_processing:
Sequence reads were mapped to hg19 using STAR
Read count calculation was performed by RSEM
Assembly: hg19

growth_protocol: RH30 cells were grown in RPMI supplemented with 10% FBS (Gibco, Life Technologies), 10mM HEPES, 100U/mL penicillin, 100 μg/ml streptomycin and 2mM L-glutamine (Gibco, Life technologies)

extract_protocol:
RNA was extracted using RNAeasy kits (Qiagen Cat# 74104, Hilden, Germany)
RNA-Seq libraries were constructed using Illumina TruSeq stranded mRNA sample preparation kits

treatment_protocol: RH30 cells were treated with 30 µM of piperacetazine or DMSO for 24 hours before harvest for RNA

value: human rhabdomyosarcoma cell line

value: PAX3-FOXO1 positive

value: DMSO

tag: treatment duration

value: 24 hours


title: Tfcp2l1 KO Post Flu Sample 1


title: T051 [HA_019]


title: T042 [HA_018]


title: U3013,glioblastoma, cells [SMAD3_U3013 Cut&Run]

value: proneural

value: WT


title: U3009,glioblastoma, cells [SMAD3_U3009 Cut&Run]


title: RH30_DMSO_24h_r1_200108_T

description: control sample biological replicate 1


title: T041 [HA_017]


title: Wildtype Post-flu Sample 5

value: Sftpc-creERT2; R26R_EYFP


title: U3008,glioblastoma, cells [SMAD3_U3008 Cut&Run]

value: neural


title: T012 [HA_016]


title: RH30_Inhibitor6_30uM_24h_200108_T

description: experimental sample

value: 30 µM of piperacetazine


title: Wildtype Post-flu Sample 4


title: AM7_07_Control_INPUT

city: Manchester

first: Tim

middle: C

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

country: United Kingdom

institute: Cancer Research UK

data_processing:
Reads were aligned to the human genome (GRCh38 GENCODE release 25) using BWA-MEM version 0.7.15 (Li and Durbin 2009). Reads were filtered using Samtools (version 0.1.9) (Li et al., 2009) to keep only reads that mapped to standard chromosomes and Bedtools version 2.25.0 (Quinian and Hall, 2010) to remove reads mapped to blacklisted regions defined by ENCODE (http://mitra.stanford.edu/kundaje). Peaks were called with Model-based Analysis of ChIP-Seq version 2 (MACS2) using the following parameters -f BAMPE, --keep-dup 5 to keep only paired-end reads with up to 5 duplicates (Zhang et al. 2008). Annotation of peaks was performed with Homer version 4.10 (Heinz et al. 2010).
Assembly: GRCh38

source_name: H441 cell line

growth_protocol: H441 cells were cultured in RPMI-1640 Medium (Sigma-Aldrich), supplemented with 10% FBS and 1% penicillin/streptomycin (Gibco).

extract_protocol:
Chromatin immunoprecipitation was performed using the SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) (Cell Signalling Technology) following the instructions of the manufacturer. 10 μg of chromatin was incubated overnight with 1.6μg of the sheep anti-TIAM1, rabbit anti-TRIM28 or rabbit anti-H3K9me3 antibody.
ChIP-seq libraries were prepared using 1ng of ChIP DNA and 12 cycles of amplification with the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, Cat No:  E7645L). Libraries were quantified by qPCR using a KAPA Library Quantification Kit for Illumina sequencing platforms (Roche, Cat No: 07960336001). Paired-end 75bp sequencing was carried out by clustering 1.7pM of the pooled libraries on a NextSeq 500 sequencer (Illumina Inc.).


title: U3042,glioblastoma, cells [SMAD3_U3042 Cut&Run]


title: T011 [HA_015]


title: T342 [HA_014]


title: AM7_03_TRIM28_CHIP_Control

value: anti-TRIM28 (ab10484, abcam, 1.6μg


title: hAstro, control, cells [SMAD3_hAstrocytes Cut&Run]

source_name: hAstro

value: hAstro

value: normal human astrocytes


title: U3121,glioblastoma, cells [PITX1_U3121 Cut&Run]

value: mesenchymal


title: T341 [HA_013]

value: mammary carcinoma


title: AM6_06_Rep_3_TIAM1_KD

data_processing:
Reads were aligned to the human genome (GRCh38 GENCODE release 25) and gene annotated with their corresponding GTF file (GENCODE GRCh38 release 25) using STAR version 2.4.2a with the settings --outFilterMultimapNmax 20 ,--outFilterType BySJout, --alignSJoverhangMin 8, --quantMode GeneCounts (Dobin A, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21). DEseq2 was used to perform differential gene expression analysis and calculate FPKM (fragments per kilobase of transcript per million mapped reads) values for each gene (Love et al., 2014).
Assembly: GRCh38

extract_protocol:
RNA was extracted from cells using the RNeasy Kit (Qiagen) following the instructions of the manufacturer. Indexed PolyA libraries were prepared using 200ng of total RNA and 14 cycles of amplification with the Agilent SureSelect Strand Specific RNA Library Prep Kit for Illumina Sequencing (Agilent, Cat No: G9691B).
Libraries were quantified by qPCR using a Kapa Library Quantification Kit for Illumina sequencing platforms (Roche, Cat No: 07960336001). Single read 75bp sequencing was carried out by clustering 2.0pM of the pooled libraries on a NextSeq 500 sequencer (Illumina Inc.).

tag: source tissue

value: lung tumour


title: M4

city: East Lansing

first: Hua

last: Xiao

state: Michigan

address: 567 WILSON RD, RM 2201

department: Physiology

institute: Michigan State University

description:
cDNA library synthesized by mRNA template enriched from total RNA
macrophages with Ncoa5 deletion from experimental mouse4

data_processing:
Raw data was delivered by Novogene. Approximately 90 million reads were generated for each sample.
Raw data was then filtered and quality-controlled using fastp 0.21.0 with the default settings.
Data quantification was performed using Salmon 1.3.0 with the mapping-based mode and with a salmon index built using Gencode mouse release M25 (GRCm38.p6).
The gene expression analysis was performed using DESeq2 1.28.1.
Gene expression table was generated using DESeq2 normalized counts.
Genome_build: Gencode mouse release M25 (GRCm38.p6)
Supplementary_files_format_and_content: zip files are compressed final Salmon outputs for each sample. csv file contains DESeq2 normalized counts for all samples.

source_name: liver F4/80+ non-parenchymal cells

growth_protocol: All mice were housed in Optimice cages at Michigan State University animal facility on a 12:12-h light-dark cycle and fed standard rodent diet ad libitum

extract_protocol:
Liver non-parenchymal cells were isolated in a two-step perfusion procedure. The hepatocytes were removed by centrifugation and F4/80+ cells were isolated from non-parenchymal cells using Anti-F4/80 MicroBeads (130-110-443, Miltenyi Biotec) according to the protocol supplied by the manufacturer. High-quality RNA was prepared from F4/80+ non-parenchymal cells using a combined TRIzol and RNeasy Mini Kit (Qiagen) method. RNA quality control was performed using the Nanodrop Spectrophotometer (Thermo Fisher) and TapeStation System (Agilent).
250~300bp insert cDNA library preparation was carried out by Novogene. Generally mRNA was enriched using oligo(dT) beads. mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment. (Method provided by Novogene)

tag: tissue

value: liver

value: Ncoa5flox/+ LyzMcre/+

value: 6.5 month

value: F4/80+ non-parenchymal cells (Kupffer cells, macrophages)


title: T312 [HA_012]

tag: cell type

value: nanoparticle


title: U3086,glioblastoma, cells [PITX1_U3086 Cut&Run]

value: classical

tag: genotype


title: U3118,glioblastoma, cells [PITX1_U3118 Cut&Run]

value: proneural

tag: treatment


title: T311 [HA_011]


title: U3085,glioblastoma, cells [PITX1_U3085 Cut&Run]

tag: cell line

value: WT


title: OPC, control, cells [SMAD3_OPC Cut&Run]

source_name: OPC

value: OPC

value: oligodendrocyte precursor cells


title: Wildtype Post-flu Sample 6

first: Michael

value: Lung

value: Sftpc-creERT2; R26R_EYFP

value: 14 day post flu


title: M3

description:
cDNA library synthesized by mRNA template enriched from total RNA
macrophages with Ncoa5 deletion from experimental mouse3


title: AM6_05_Rep_3_control_S5


title: M2

description:
cDNA library synthesized by mRNA template enriched from total RNA
macrophages with Ncoa5 deletion from experimental mouse2


title: AM6_04_Rep_2_TIAM1_KD


title: T302 [HA_010]

tag: time


title: Wildtype Post-flu Sample 3


title: M1

description:
cDNA library synthesized by mRNA template enriched from total RNA
macrophages with Ncoa5 deletion from experimental mouse1


title: T301 [HA_009]


title: U3073,glioblastoma, cells [PITX1_U3073 Cut&Run]


title: C4

description:
cDNA library synthesized by mRNA template enriched from total RNA
control macrophages from control mouse4

value: Ncoa5flox/+ LyzM+/+


title: AM6_02_TIAM1_KD


title: AM7_01_H3K9me3_CHIP_Control

value: anti-H3K9me3 (D4W1U (#139695), Cell Signaling, 1.6 μg)


title: T283 [HA_008]

value: mammary carcinoma


title: T282 [HA_007]


title: AM6_03_Rep_2_control

value: lung tumour


title: U3054,glioblastoma, cells [PITX1_U3054 Cut&Run]

value: mesenchymal


title: Wildtype Post-flu Sample 1


title: C3

description:
cDNA library synthesized by mRNA template enriched from total RNA
control macrophages from control mouse3

value: liver


title: AM6_01_Control


title: AM7_05_Tiam1_CHIP_Control

value: anti-TIAM1 (AF5038, R&D systems,


title: UCLA1_hTET1_CDKO1312_hESC_bACEseq

first: Fei-Man

last: Hsu

address: 610 Charles E Young Dr S

department: MCDB

data_processing:
FastQC was used to check the quality of the sequencing reads.  After adaptor trimming with Cutadapt, read pairs with length above 30bp were kept, and aligned to the 3-letter human reference genome GRCh38 using bsbolt Align with default setting.  Methylation calling was done using bsbolt CallMethylation and only CpG sites with depth >= 4 were kept.  Common CpG sites among each libraries were extracted with bsbolt AggrgateMatrix with --min-sample 1.0.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files.

extract_protocol:
tion was carried out using EZ DNA Methylation-Direct™ Kit (Zymo Research Cat# D5020).  Eluate was denatured at 95°C and snap cooled by transfer to a PCR tube rack pre-incubated at −80°C.   After thawing, 1.5μL 40mM MES pH 6.0 + 0.1% Tween and 1.5μL 50μM A3A were added to each reaction to a final volume of 15μL. The deamination reactions were incubated at 37°C for 2h, purified with 1.6x homebrew SPRI beads and eluted.  After deamination, the samples were prepared for Illumina sequencing using the Accel Methyl-NGS kit (Swift Biosciences).
bACEseq

value: hESC

value: TET1 catalytic domain knockout


title: U3042,glioblastoma, cells [PITX1_U3042 Cut&Run]

value: classical


title: T292 [HA_006]

value: nanoparticle


title: U3031,glioblastoma, cells [PITX1_U3031 Cut&Run]

value: WT


title: C1

description:
cDNA library synthesized by mRNA template enriched from total RNA
control macrophages from control mouse1

value: 6.5 month

value: F4/80+ non-parenchymal cells (Kupffer cells, macrophages)


title: UCLA1_hTET1_CDKO1105_hESC_bACEseq


title: UCLA1_hTET1_CDKO1102_hESC_bACEseq


title: U3013,glioblastoma, cells [PITX1_U3013 Cut&Run]

value: proneural


title: T221 [HA_003]


title: T291 [HA_005]


title: U3078,glioblastoma, cells [PITX1_U3078 Cut&Run]


title: C2

description:
cDNA library synthesized by mRNA template enriched from total RNA
control macrophages from control mouse2


title: T222 [HA_004]


title: mouse NGFR Lv16

city: New York

first: Caghan

last: Kizil

institute: Columbia University Irving Medical Center

description: 10X Chromium, single-cell sequencing

data_processing:
The fastq files were aligned to mouse genome (mm10) and (ensemble transcripts from Ensembl Version 98) by using STAR. The BAM files were as input for Cell Ranger (10X genmoics) to generate processed data files that include gene names (row names) and cell names (column names) and counts. Further analysis done by using Seurat package in R.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file, with gene names in rows and cell names and counts in columns.

source_name: hippocampus

growth_protocol: Mice were kept under pathogen-free conditions on a strict 12 hour alternating light and dark cycle with standard mouse food (chow) and water ad libitum. They were group-housed in standard ventilated cages prior to the experiments and were kept in individual cages after surgical procedures.

extract_protocol:
Cells from mouse hypocampus were dissociated and mCherry positive cells were sorted.  The library preparation was performed by 10X Genomics as per manufactur protocol
10X genomics

treatment_protocol: The viral injections of p6NST90-hUb-mNGFR-T2A-mCherry-Lv16 (Lv16) or p6NST90-hUb-mCherry-Lv13 (Lv13) were carried into wild type mouse brains in an S2-approved laboratory. Fixed gender mice of age 28 weeks were used. All the regulated precautions were met to prevent the direct contact of personnel with viruses and to avoid infecting the animal during the operation. The procedure was carried out according to previously established protocol (Artegiani et al., 2011). During the entire surgery, the mice were anesthetized using a mix of oxygen and isoflurane (49:1) (Baxter – HDG9623) flow and placed on a pre-warmed heat-pad to prevent hypothermia. 1 µl of the respective virus was injected at the coordinates: (a) ± 1.6 mm mediolateral, −1.9 mm anterior-posterior and −1.9 mm dorsoventral from the Bregma for the hippocampus at 200 nl/min speed; and (b) ± 1.0 mm mediolateral, −1.0 mm anterior-posterior and −0.8 mm dorsoventral from pia for the cortex at 50 nl/min speed. Contralateral hemispheres of wild type animals were used for injecting p6NST90-hUb-mNGFR-T2A-mCherry-Lv16 (Lv16) or p6NST90-hUb-mCherry-Lv13 (Lv13) viruses. At 3 days post-injection, mice were sacrificed via cervical dislocation followed by hippocampi extraction. Isolated hippocampi were kept on ice until dissociated into cells which were used for the single-cell sequencing.

value: wild type

value: brain (hippocampus)

value: mouse mCherry NGFR virus (Lv16)


title: Wildtype Post-flu Sample 2

value: Lung

value: Sftpc-creERT2; R26R_EYFP

value: 14 day post flu


title: UCLA2_D4hPGCLC_rep3_bACEseq

value: hPGCLC

value: wild-type


title: U3009,glioblastoma, cells [PITX1_U3009 Cut&Run]


title: J4_1

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

description:
J4_S6
scRNA-seq of Sus scrofa: 8 weeks old female jejunum collected at location of distal-most discrete Peyer's patch

data_processing:
Read were aligned using Cell Ranger v6.1.2 (single-cell) and Space Ranger v1.3.0 (spatial)
Assembly: Sus Scrofa 11.1
Annotation build: Sus Scrofa 11.1.97

organism: Sus scrofa

source_name: Jejunum

extract_protocol:
Single-cell RNA sequencing: Reagents were equilibrated and processes carried out at room temperature (RT) unless stated otherwise. ~2-inch-length tissue cross-sections were placed into 30 mL of 2 mM ethylenediaminetetraacetic acid (EDTA; Invitrogen AM9260G), 2 mM L-glutamine (Gibco 25-030), 0.5% bovine serum albumin (BSA; Sigma-Aldrich A9418) in Hank’s balanced salt solution (HBSS; Gibco 14175) for transport. Tissues were cut open, rinsed with phosphate-buffered saline (PBS), pH 7.2 (made in-house), the muscularis layer was removed, and ~1.5 g of tissue was incubated in 30 mL of 5 mM dithiothretol (Invitrogen 15508), 2% fetal calf serum (FCS; heat-inactivated; Gibco A38401) in HBSS for 20 min, 37C, 200 rpm. Tissues were washed in 20 mL of 10 mM HEPES (Fisher BioReagents BP299) in HBSS for 10 min, 37C, 200 rpm, followed by transfer into a C-tube (Miltenyi 130-093-237) containing 15 mL of 10 mM HEPES, 0.2U/mL Liberase TM (Roche 5401127001), 30 ug/mL DNase I (Sigma D5025) in HBSS. Mechanical dissociation was executed with a gentleMACs Octo Dissociator (Miltenyi 130-095-937) intestine C-tube protocol. C-tubes were incubated 45 min, 37C, 200 rpm, followed by another round of mechanical dissociation. 10 mL of 2 mM EDTA, 2 mM L-glutamine, 0.5% BSA in HBSS was added to C-tubes, and samples were filtered sequentially through non-woven surgical gauze sponges (Starryshine GZNW44), 100-micron nylon filters, and 40-micron nylon filters. Collected suspensions were centrifuged 5 min, 200 xg and resuspended in 2 mM L-glutamine, 2% FCS in HBSS. Density gradient centrifugation was performed to enrich for lymphocytes by overlaying cell suspensions onto Histopaque 1077 (Sigma-Aldrich) and centrifuging 30 min, 400 xg, 22C. Cell fractions were collected from the interphase layer and washed with 2 mM L-glutamine, 2% FCS in HBSS. Final cell suspensions were poured over 40-micron nylon filters.
Tissues were embedded in optimal cutting temperature (OCT) compound (Sakura 4583) and snap frozen in an isopentane bath cooled with liquid nitrogen. Tissues were stored at -80C. For cryosectioning, tissue blocks were equilibrated to -20C for 20 minutes. On a cryostat (Leica CM 1860), OCT blocks were cut and faced to an appropriate plane and size that included transverse profiles of Peyer’s patches, lamina propria, and epithelium. 10-micron tissue sections were adhered to VIsium slides (10X Genomics).
Single-cell RNA sequencing: A target of 10,000 isolated cells per sample were partitioned using the Chromium Single Cell 3’ v3 Chemistry (10X Genomics CG000183). Samples were sequenced using 2x100, paired-end sequencing on a HiSeq 3000 and NovaSeq SP flow cell (Illumina).
Spatial transcriptomics: Using optimized permeabilization parameters, libraries were created using the Visium Spatial Gene Expression Reagent Kit (10X Genomics PN-1000186), Visium Spatial Gene Expression Slide Kit (10X Genomics PN-1000185), and Library Construction Kit (10X Genomics PN-1000190) according to procedures in User Manual CG000239 (10X Genomics). Tissue bluing was omitted from the manufacturer’s protocol. Tissue images were digitally scanned without coverslips by an Aperio AT2 whole slide imager (Leica Biosystems) at 40X (0.25 um/pixel) magnification. Samples were sequenced on a NovaSeq SP flow cell (Illumina) with 2x100, paired-end sequencing.

value: Jejunum

tag: tissue dissection

value: Jejunum collected at location of distal-most discrete Peyer's patch

tag: breed

value: Mixed-breed

value: 8 weeks

value: Female


title: IFT20 floxed Cre Positive 3M #4

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Transcriptome profile of mutant tissue at 3 months, biological rep4

data_processing:
Sequence reads were trimmed using bbduk software(https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/usage-guide/) (bbmap suite 37.31) to remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6) and then aligned on mm10 reference sequence using STAR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: Retinal Pigment Epithelial Cells (Isolated)

growth_protocol: The morning after mating was considered as embryonic day (E) 0.5 and up to 24 h after birth was considered as postnatal day (P) 0. 3 M is three months. Animals were sacrificed by cervical dislocation. Generation and genotyping of IFT20-Floxed and DCT-Cre mice  was previously described. Jonassen et al., 2008 Journal of Cell Biology and Davis et al., 2009 Journal of Developmental Biology

extract_protocol:
RNA was quantified and mixed at 10ng/µl
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NovaSeq500 (Illumina) with a read length of 100 bp

treatment_protocol: No treatment was performed

value: Three Months - Isolated RPE cells

tag: gender

value: not collected

tag: background strain

value: Mixed


title: J3_1

description:
J3_S5
scRNA-seq of Sus scrofa: 8 weeks old female jejunum collected at location of distal-most discrete Peyer's patch

tag: age


title: UCLA2_D4hPGCLC_rep2_bACEseq

city: Los Angeles


title: OPC, control, cells [PITX1_OPC Cut&Run]

value: OPC

value: oligodendrocyte precursor cells

value: WT


title: U3008,glioblastoma, cells [PITX1_U3008 Cut&Run]

value: neural


title: IFT20 floxed Cre Positive 3M #3

description: Transcriptome profile of mutant tissue at 3 months, biological rep3


title: J2_1

description:
J2_S4
scRNA-seq of Sus scrofa: 8 weeks old female jejunum collected at location of distal-most discrete Peyer's patch


title: UCLA2_D4hPGCLC_rep1_bACEseq


title: primary Delta vdj library

description:
RC048, RC079, RC214, RC182, RC156, RC242, RC113, RC281, RC362, RC396
pd.barcodes.tsv.gz
pd.matrix.mtx.gz
pd.features.tsv.gz

data_processing:
the demultiplexing, barcoded processing, gene counting and -multi were made using cell ranger (https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/tutorial/tutorial-multi)
data were analyzed using Seurat v4.1.3
Supplementary files format and content: tab-separated values and matrix files

extract_protocol:
GEM generation and RT
Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) User Guide with Feature Barcode technology for Cell Surface Protein & Immune Receptor Mapping

value: pbmc


title: IFT20 floxed Cre Positive 3M #2

description: Transcriptome profile of mutant tissue at 3 months, biological rep2


title: hAstro, control, cells [PITX1_hAstrocytes Cut&Run]

value: hAstro

value: normal human astrocytes


title: IFT20 floxed Cre Positive 3M #1

description: Transcriptome profile of mutant tissue at 3 months, biological rep1


title: I4_1

description:
I4_S3
scRNA-seq of Sus scrofa: 8 weeks old female distal ileum with Peyer's patches

source_name: Ileum

value: Ileum

value: Distal ileum with Peyer's patches


title: OPC, rep2 (RNAseq)

description: counts.txt matrix column 'hAstro_R2'

data_processing:
Sequence reads were mapped to hg38 using  STAR (options: --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 12 --outFilterScoreMinOverLread 0.3 --alignSJoverhangMin 15 --outFilterMismatchNmax 33 --outFilterMatchNminOverLread 0 --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif --quantMode GeneCounts)
Read count extraction and normalization were performed using R package DeSEQ2
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts

growth_protocol: OPCs (Creative Biolabs CAT#: NCL-2103-P49) were cultured in Oligodendrocyte Precursor Cell Growth Medium [CAT#: NCL-21P6-106] in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation module (E7490) and NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770) with NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, E6440S)  following manufacturer's protocols.


title: UCLA2_hESC_rep3_bACEseq

value: hESC

value: wild-type


title: UCLA2_hESC_rep2_bACEseq


title: Control Lv13

description: 10X Chromium, single-cell sequencing

value: wild type

value: brain (hippocampus)

value: Control mCherry virus (Lv13)


title: OPC, rep1 (RNAseq)

description: counts.txt matrix column 'hAstro_R1'


title: Control: Cre Positive 3M #4

description: Transcriptome profile of control tissue at 3 months , biological rep4

value: Three Months - Isolated RPE cells


title: Input_ChIP_OPC

data_processing:
Raw reads were mapped to the human genome (hg38, Ensembl genome version 96, ensembl.org) using bowtie2 (options: -f BAMPE --threads 4 --very-sensitive).
Enriched peaks were called using MACS2 (options: -f BAMPE --broad -g hs -B -q 0.05).
For the input (-c) the analysis was done as follows: Astrocytes were paired with the Astrocyte-input, classical-subtype cell lines qith the classical-input, mesenchymal cell lines with mesenchymal-input and neural or proneural cell lines with Neural/Proneural-input.
Assembly: hg38
Supplementary files format and content: bed files (except for Input sample)

extract_protocol:
Approximately 3-6 million cells were cross-linked with 1% formaldehyde for 15 minutes
After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris) for 12 minutes, IP was done with 4ug of anti-H3K27Ac: ab4729 or anti-H3K27me3: ab8580
About 10ng of immunoprecipitated DNA from H3K27Ac/ H3K27me3-ChIP was used to prepare libraries using NEBNext Ultra II DNA Library Prep Kit for Illumina, E7645L and NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs), E6440S.


title: UCLA1_D4hPGCLC_rep2_bACEseq

value: hPGCLC


title: I3_1

description:
I3_S2
scRNA-seq of Sus scrofa: 8 weeks old female distal ileum with Peyer's patches

value: Mixed-breed

value: 8 weeks

value: Female


title: F2 generation (both parents being representatives of the F1 generation with C. gibelio mtDNA), infected group, repl. 3

description: gibel.featureCounts.tsv

data_processing:
Quality check (FastQC v. 0.11.9)
Quality trimming (Trimmomatic v. 0.36, CROP:250 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:35)
Alignment (STAR v. 2.7.3a; employing default parameters, except for --outFilterMismatchNoverLmax 0.1 and --twopassMode Basic)
Quality control after alignment concerning the number and percentage of uniquely- and multi-mapped reads, rRNA contamination, the mapped regions, the read coverage distribution, strand specificity, gene biotypes, and PCR duplication was performed using several tools (RSeQC v. 2.6.2; Picard toolkit v. 2.18.27; Qualimap v. 2.2.2; BioBloom tools v. 2.3.4)
DGE analysis (featureCounts v. 1.6.3 with settings -s 2 -T 10 -F GTF -Q 0 -d 1 -D 25000; DESeq2 v1.20.0)
Functional annotation (KEGG pathway database; clusterProfiler v 3.12.0)
Assembly: ASM336829v1, GCA_000951615.2
Supplementary files format and content: tab-delimited text file with featureCounts for samples that originated and mapped significantly better on the C. carpio reference genome
Supplementary files format and content: tab-delimited text file with featureCounts for samples that originated and mapped significantly better on the C. gibelio reference genome

organism: Carassius gibelio x Cyprinus carpio 'xingguonensis'

extract_protocol:
NEBNext Poly(A) mRNA Magnetic Isolation Module
NEBNext Ultra Directional RNA Library Prep Kit for Illumina

value: Head kidney


title: UCLA1_D4hPGCLC_rep3_bACEseq


title: I2_1

description:
I2_S1
scRNA-seq of Sus scrofa: 8 weeks old female distal ileum with Peyer's patches


title: Control: Cre Positive 3M #2

description: Transcriptome profile of control tissue at 3 months , biological rep2

value: not collected

value: Mixed


title: Control: Cre Positive 3M #3

description: Transcriptome profile of control tissue at 3 months , biological rep3


title: UCLA1_D4hPGCLC_rep1_bACEseq


title: H3K27Me3_ChIP_OPC

value: OPC

value: oligodendrocyte precursor cells

value: WT


title: F2 generation (both parents being representatives of the F1 generation with C. gibelio mtDNA), infected group, repl. 2

description: gibel.featureCounts.tsv


title: Control: Cre Positive 3M #1

description: Transcriptome profile of control tissue at 3 months , biological rep1


title: F2 generation (both parents being representatives of the F1 generation with C. gibelio mtDNA), infected group, repl. 1

description: gibel.featureCounts.tsv


title: OPC cell line (ATACseq)

data_processing:
Then, the raw read files were trimmed with cutadapt to remove the Nextera sequence, 5’CTGTCTCTTATACACATCT3’ prior to map them to hg38 using bowtie2 (--threads 8 -k 2 --local --maxins 2000)
reads were filtered with samtools -view with flag -q 10, to remove all reads having a MAPQ lower than 10
peaks were called by MACS2, for broad peaks by keeping the flags -f BAMPE (for a valid paired-end aligned .bam file), --broad, -q 0.05 --shift 100 --extSize 200 against baseline.
Assembly: hg38
Supplementary files format and content: bed files

extract_protocol:
For ATAC-seq, an exact number of 50,000 cells for each of the 16 cell lines were used to tagment DNA using Illumina Tagment DNA TDE1 Enzyme and Buffer Kits (small) (Illumia #20034197).
Exactly 5uL of tagmented DNA from each line was amplified with NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs #M0541S). Custom oligos and adapters were designed and used for library amplification.
Fragmentation of the libraries were assessed by running Bioanalyzer High Sensitivity DNA Analysis (Agilent # 5067-4626) and were sent to be sequenced at Novogene.


title: H3K27Ac_ChIP_OPC


title: F2 generation (both parents being representatives of the F1 generation with C. gibelio mtDNA), control group, repl. 2

description: gibel.featureCounts.tsv


title: U3028,glioblastoma, cells [PITX1_U3028 Cut&Run]

data_processing:
library strategy: Cut and Run
Raw reads were mapped to the human genome (hg38, Ensembl genome version 96, ensembl.org) using bowtie2 (options: -f BAMPE --threads 4 --very-sensitive).
Enriched peaks were called using MACS2 (options: -f BAMPE --broad -g hs -B -q 0.05).
Peaks were called on the target data at 1% of regions with enriched signals using SEACR with the following parameters: 0.01 norm stringent
Assembly: hg38
Supplementary files format and content: bed files

extract_protocol:
Approximately 100 thousend cells were cross-linked with 0.1% formaldehyde for 2 minutes
After quenching and cell lysis, CUT&RUN Assay kit (#86652, Cell Signaling Technologies) instructions were followed and  IP was done with either 1.2ug of  SMAD3 (Abcam #ab208182), or 4ug of PITX1 (Santa Cruz, #sc-271435 X)
Libraries were prepared using the DNA library Prep Kit for illumine(Cell Signaling Technologies #56795).

value: classical


title: IFT20 floxed Cre Positive P29 #2

description: Transcriptome profile of mutant tissue at P29, biological rep2

value: Post natal day 29 - Isolated RPE cells


title: IFT20 floxed Cre Positive P29 #4

description: Transcriptome profile of mutant tissue at P29, biological rep4


title: UCLA1_hESC_rep1_bACEseq

value: hESC

value: wild-type


title: F2 generation (both parents being representatives of the F1 generation with C. gibelio mtDNA), control group, repl. 3

description: gibel.featureCounts.tsv


title: IFT20 floxed Cre Positive P29 #3

description: Transcriptome profile of mutant tissue at P29, biological rep3


title: PC3_5_0_Era_3

city: nan ning

first: 周

last: 青鸟

address: shaungyonglu street num 22

institute: Guangxi Medical University

description:
treatment
PC3_group_gene_fpkm.txt

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Prostate

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Prostate

value: Prostate cancer cells


title: UCLA1_hTET1_CDKO1312_hESC_WGBS

extract_protocol:
Genomic DNA from hESC and hPGCLC were extracted with Quick-DNA mini prep kit (Zymo Research, Cat# D3025).
tion was carried out using EZ DNA Methylation-Direct™ Kit (Zymo Research Cat# D5020).  After bilfite conversion, the samples were prepared for Illumina sequencing using the Accel Methyl-NGS kit (Swift Biosciences).

value: TET1 catalytic domain knockout


title: UCLA1_hTET1_CDKO1105_hESC_WGBS


title: maternal backcross (backcross F1 hybrid x C. gibelio), infected group, repl. 3

description: gibel.featureCounts.tsv


title: PC3_5_0_Era_2

description:
treatment
PC3_group_gene_fpkm.txt


title: maternal backcross (backcross F1 hybrid x C. gibelio), infected group, repl. 2

description: gibel.featureCounts.tsv


title: UCLA1_hESC_rep3_bACEseq


title: IFT20 floxed Cre Positive P29 #1

description: Transcriptome profile of mutant tissue at P29, biological rep1


title: UCLA2_D4hPGCLC_rep3_WGBS

value: hPGCLC


title: UCLA1_hTET1_CDKO1102_hESC_WGBS


title: F2 generation (both parents being representatives of the F1 generation with C. gibelio mtDNA), control group, repl. 1

description: gibel.featureCounts.tsv


title: maternal backcross (backcross F1 hybrid x C. gibelio), infected group, repl. 1

description: gibel.featureCounts.tsv


title: UCLA2_D4hPGCLC_rep2_WGBS


title: maternal backcross (backcross F1 hybrid x C. gibelio), control group, repl. 4

description: gibel.featureCounts.tsv


title: Controrl: Cre Positive P29 #1

description: Transcriptome profile of control tissue at P29 , biological rep1


title: UCLA2_hESC_rep3_WGBS


title: maternal backcross (backcross F1 hybrid x C. gibelio), control group, repl. 2

description: gibel.featureCounts.tsv


title: maternal backcross (backcross F1 hybrid x C. gibelio), control group, repl. 1

description: gibel.featureCounts.tsv


title: IFT20 floxed Cre Positive P11 #4

description: Transcriptome profile of mutant tissue at P11, biological rep4

value: Post natal day 11 - Isolated RPE cells


title: Controrl: Cre Positive P29 #4

description: Transcriptome profile of control tissue at P29 , biological rep4


title: IFT20 floxed Cre Positive P11 #3

description: Transcriptome profile of mutant tissue at P11, biological rep3


title: paternal backcrosses (backcross F1 hybrid x C. carpio), infected group, repl. 3

description: gibel.featureCounts.tsv


title: Controrl: Cre Positive P29 #2

description: Transcriptome profile of control tissue at P29 , biological rep2


title: UCLA2_D4hPGCLC_rep1_WGBS


title: UCLA2_hESC_rep1_WGBS


title: maternal backcross (backcross F1 hybrid x C. gibelio), control group, repl. 3

description: gibel.featureCounts.tsv


title: Controrl: Cre Positive P29 #3

description: Transcriptome profile of control tissue at P29 , biological rep3


title: paternal backcrosses (backcross F1 hybrid x C. carpio), infected group, repl. 4

description: gibel.featureCounts.tsv


title: UCLA1_D4hPGCLC_rep3_WGBS


title: IFT20 floxed Cre Positive P11 #1

description: Transcriptome profile of mutant tissue at P11, biological rep1


title: UCLA1_D4hPGCLC_rep2_WGBS


title: paternal backcrosses (backcross F1 hybrid x C. carpio), control group, repl. 4

description: gibel.featureCounts.tsv


title: UCLA1_hESC_rep3_WGBS


title: paternal backcrosses (backcross F1 hybrid x C. carpio), control group, repl. 3

description: gibel.featureCounts.tsv


title: paternal backcrosses (backcross F1 hybrid x C. carpio), infected group, repl. 2

description: gibel.featureCounts.tsv


title: UCLA2_hESC_rep2_WGBS


title: IFT20 floxed Cre Positive P11 #2

description: Transcriptome profile of mutant tissue at P11, biological rep2


title: UCLA1_hESC_rep2_WGBS


title: KPP_replicate_2

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

description: single-nuclei

data_processing:
Cell Ranger v3.1.0 (10x Genomics) was used using the count function with default parameters for read alignment, demultiplexing, and quantification of gene counts per cell. Data was aligned to a custom mm10 reference integrating the different vectors added to the mouse genome. Five custom chromosomes were added to the mm10 genome, the first one containing the piggybac transferase; the second one containing Akaluc and the GFP sequences; the third one containing the human H3F3A gene with HA tag; the fourth one containing the p53 guide RNA and the last one containing the shATRX sequence.
Reads mapping to these sequences were counted using a custom GTF file supplied to Cell Ranger.
To identify cell populations shared by KNF and KPP samples, samples were integrated using Harmony v1.0. Due to imbalanced cell numbers between genotypes, each KNF replicate was first downsampled to match the KPP replicates (N = 15,537), such that proportions of clusters identified in individual sample analysis were maintained. Integration of the KPPMPIK replicates was performed using Harmony v1.0.
Assembly: mm10
Supplementary files format and content: *features.tsv.gz, *barcodes.tsv.gz, *matrix.mtx.gz: compressed filtered features (genes and peaks), barcodes and expression matrices generated by Cell Ranger.
Supplementary files format and content: cell_metadata_KPP_KNF.tsv and cell_metadata_KPPMPIK.tsv: tab-separated files containing cell information for each sample. Columns definition: cell: cell barcode as in counts matrix suffixed with sample number; alias: Sample alias; nCount_RNA: number of UMIs per cell; nFeature_RNA: number of genes detected; percent_mito: percent mitochondrial content; percent_ribo: percent ribosomal content; cluster: cluster number based on SNN algorithm from Seurat; consensus_label: cell type label; consensus_class: cell class

molecule: nuclear RNA

source_name: Hindbrain

extract_protocol:
RNA was extracted using the Rneasy Plus Kit (Qiagen) according to the manufacturer's instructions. RNA quality and quantification were carried out using a Nanodrop spectrophotometer (Thermo Fisher) or a Bioanalyzer (Agilent). Total RNA (500 ng) was used for reverse transcription using TaqMan Reverse Transcription Reagents (Thermo Fisher), and real-time PCR was performed using the SsoAdvanced Universal SYBR Green Supermix (Bio-Rad) on a CFX96 Touch Real-Time PCR Detection System (Bio-Rad; RRID:SCR_018064).
Microdissected tissue was enzymatically digested into a single-cell suspension using the Papain Dissociation System according to the manufacturer’s instructions (Worthington Biochemicals). The samples were sequenced using the 10X Chromium single-cell 3' protocol.

treatment_protocol: In uteroelectroporation was performed using sterile technique on isoflurane/oxygen-anesthetized pregnant females at E12.5. Analgesic support was also provided pre-emptively (subcutaneous delivery of Vetergesic and Carpofen at 0.1 mg/kg and 5 mg/kg, respectively). Uterine horns were exposed through a 1 cm incision and individual embryos were digitally manipulated into the correct orientation for intraventricular injection. Pulled borosilicate capillaries were loaded with endotoxin-free DNA and Fast Green dye (0.05%, Sigma) for visualisation, and a microinjector (Eppendorf) was used to inject either the lateral or fourth ventricles with the DNA-dye mixture. 3–5 plasmids were injected simultaneously, each at a final concentration of 2 µg/µl and 1–2 µl of total solution was injected per embryo. DNA was electroporated into cortical neural progenitors using 5 mm tweezertrodes (BTX), or into lower rhombic lip progenitors using 3 mm tweezertrodes, applying 5 square pulses at 35 V, 50 ms each with 950 ms intervals. The embryos were returned into the abdominal cavity, the muscle and skin were sutured and the animal was monitored until fully recovered from the procedure.

value: Hindbrain

value: brain tumor

tag: strain

value: H3.3K27M, P53 LOF, PDGFRA WT overexpression

tag: Sex

value: female


title: scRNA-seq BMSCs

first: Junji

last: Xu

address: 9000 Rockville Pike

institute: NIH, NIDCR

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger v2.1.1 pipeline using default settings.
Secondary analysis was performed using 10X Genomics Loupe Cell Browser v2.0.0
Genome_build: GRCh38
Supplementary_files_format_and_content: CellRanger v2.1.1 gene counts matrices.

source_name: Bone marrow mesenchymal stromal cells

growth_protocol: pulp was separated from a remnant crown and then digested in a solution of 3 mg/ml collagenase type I (Worthington Biochem, Freehold, NJ) and 4 mg/ml dispase (Roche Molecular Biochemicals) for 1 h at 37°C. Single-cell suspensions were cultured. All cells were seeded into 6-well plates with alpha modification of Eagle's medium supplemented with 20% FCS /100 μM l-ascorbic acid 2-phosphate/2 mM l-glutamine/100 units/ml penicillin/100 μg/ml streptomycin, and then incubated at 37°C in 5% CO2.

extract_protocol:
Cells were dissociated by adding 0.5% trypsin and triturated with 1 ml pipette tip for 30 seconds at 30°C.  The dissociated cells were filtered with 40 μm strainer and washed with PBS twice before adding DMEM containing 10% FBS and spun down by centrifugation at 700g rpm for 5 min at 4°C.  Cells were resuspended and kept in DMEM before processing
scRNA-seq was carried out with 10X Genomics single cell platform (10X Genomics, Pleasanton, CA. USA).  Approximately 5000 live cells after FACS in a maximum volume of 34 microliters were loaded on a 10X Genomics Chromium Controller (10x Genomics).  Chromium Single Cell 3' Library and Gel Bead Kit v2 (10X Genomics) was used for libraries preparation according to manufacturer’s instructions.  Quality of the libraries was evaluated on a Fragment Analyzer instrument (Agilent) and sequenced on a NextSeq 500 sequencer Illumina with the following paired read lengths: 26 bp Read 1, 8 bp I7 Index and 98 bp Read 2.

tag: method

value: Single cell RNA-seq

value: Bone marrow

value: mesenchymal stromal cells


title: ATRX KO3

city: London

first: Sarfraz

last: Shafiq

state: Ontario

address: Victoria Hospital, 800 commissioners road east

department: Anatomy and Cell Biology

institute: University of Western Ontario

description:
p17 all genes CTL3 vs KO3
Total forebrain RNA (10 μg) was isolated from three P17 pairs of littermate-matched AtrxFoxG1Cre and control mice using the RNeasy Mini kit (Qiagen Cat# 74104). cRNA was generated and hybridized to an Affymetrix Mouse Genome 430 2.0 Array at the London Regional Genomics Center (London, Canada).

data_processing:
Probe signal intensities were generated using GCOS1.4 (Affymetrix Inc., Santa Clara, CA) using default values for the Statistical Expression algorithm parameters and a Target Signal of 150 for all probe sets and a Normalization Value of 1.
Gene level data was generated using the RNA preprocessor in GeneSpring GX 7.3.1 (Agilent Technologies Inc., Palo Alto, CA). Data were then transformed (measurements less than 0.01 set to 0.01), normalized per chip to the 50th percentile, and per gene to control samples. Probe sets representing Atrx transcripts were removed (10 sets). The remaining probe sets were filtered by fold change ≥1.5 between control and AtrxFoxG1Cre samples, and by confidence level of P<0.05. Significantly overrepresented GO categories were determined using the Enrichr web platform

label: biotin

source_name: brain

value: brain

value: atrx ko


title: paternal backcrosses (backcross F1 hybrid x C. carpio), control group, repl. 1

description: gibel.featureCounts.tsv

value: Head kidney


title: scRNA-seq SHED

source_name: Stem cells from human exfoliated deciduous teeth

value: dental pulp

value: Stem cells


title: paternal backcrosses (backcross F1 hybrid x C. carpio), infected group, repl. 1

description: gibel.featureCounts.tsv

source_name: Head kidney


title: KPP_replicate_1

description: single-nuclei


title: Control: Cre Positive P11 #2 (Control)

description: Transcriptome profile of control tissue at P11 , biological rep2

value: not collected

value: Mixed


title: Control: Cre Positive P11 #1 (Control)

description: Transcriptome profile of control tissue at P11 , biological rep1


title: scRNA-seq ADSCs

source_name: Adipose-derived mesenchymal stromal cells

value: Adipose


title: KPPMPIK_replicate_2

description: single-nuclei

value: H3.3K27M, PIK3CA E545K, PPM1D truncated


title: Control: Cre Positive P11 #4 (Control)

description: Transcriptome profile of control tissue at P11 , biological rep4

value: Post natal day 11 - Isolated RPE cells


title: Control: Cre Positive P11 #3 (Control)

description: Transcriptome profile of control tissue at P11 , biological rep3


title: Control 3

hyb_protocol: cRNA was generated and hybridized to an Affymetrix Mouse Genome 430 2.0 Array at the London Regional Genomics Center (London, Canada).

extract_protocol: Total forebrain RNA (10 μg) was isolated from three P17 pairs of littermate-matched AtrxFoxG1Cre and control mice using the RNeasy Mini kit (Qiagen Cat# 74104).

value: control


title: maternal backcross (backcross C. gibelio x F1 hybrid), infected group, repl. 4

description: gibel.featureCounts.tsv


title: paternal backcrosses (backcross F1 hybrid x C. carpio), control group, repl. 2

description: gibel.featureCounts.tsv


title: maternal backcross (backcross C. gibelio x F1 hybrid), infected group, repl. 3

description: gibel.featureCounts.tsv


title: KPPMPIK_replicate_1

description: single-nuclei

value: Hindbrain

value: brain tumor


title: KNF_replicate_3

description: single-nuclei

value: H3.3K27M, NF1 LOF, FGFR1-N457K

value: female


title: Control 2

description:
p17 all genes CTL2 vs KO2
Total forebrain RNA (10 μg) was isolated from three P17 pairs of littermate-matched AtrxFoxG1Cre and control mice using the RNeasy Mini kit (Qiagen Cat# 74104). cRNA was generated and hybridized to an Affymetrix Mouse Genome 430 2.0 Array at the London Regional Genomics Center (London, Canada).


title: KNF_replicate_2

description: single-nuclei


title: maternal backcross (backcross C. gibelio x F1 hybrid), infected group, repl. 2

description: gibel.featureCounts.tsv


title: Control 1

description:
p17 all genes CTL1 vs KO1
Total forebrain RNA (10 μg) was isolated from three P17 pairs of littermate-matched AtrxFoxG1Cre and control mice using the RNeasy Mini kit (Qiagen Cat# 74104). cRNA was generated and hybridized to an Affymetrix Mouse Genome 430 2.0 Array at the London Regional Genomics Center (London, Canada).


title: maternal backcross (backcross C. gibelio x F1 hybrid), infected group, repl. 1

description: gibel.featureCounts.tsv


title: KNF_replicate_1

description: single-nuclei


title: maternal backcross (backcross C. gibelio x F1 hybrid), control group, repl. 4

description: gibel.featureCounts.tsv


title: maternal backcross (backcross C. gibelio x F1 hybrid), control group, repl. 3

description: gibel.featureCounts.tsv


title: Mod2_3

city: Beijing

first: Shan

last: Jiang

address: No. 16, Nanxiao Road/Street

institute: China Academy of Chinese Medical Sciences

data_processing:
Raw reads of fastq format were firstly processed using fastp
The clean reads were mapped to the reference genome using HISAT2
FPKM3 of each gene was calculatedandthe read counts of each gene were obtained by HTSeq-count
Differential expression analysis was performed using the DESeq2
PCA analysis were performedusingR(v 3.2.0) to evaluate the biological duplication of samples
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Liver

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) accordingtothemanufacturer’s protocol.
the libraries were constructedusingVAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Liver

value: model


title: maternal backcross (backcross C. gibelio x F1 hybrid), control group, repl. 1

first: Jiri

last: Vorel

description: gibel.featureCounts.tsv


title: Mod3_4


title: Mod2_1


title: maternal backcross (backcross C. gibelio x F1 hybrid), control group, repl. 2

description: gibel.featureCounts.tsv


title: Mod1_4


title: F1 generation with C. gibelio mtDNA (termed F1 C. gibelio x C. carpio), infected group, repl. 3

description: gibel.featureCounts.tsv


title: F1 generation with C. gibelio mtDNA (termed F1 C. gibelio x C. carpio), infected group, repl. 2

description: gibel.featureCounts.tsv


title: JDH3_4

value: BBBPH


title: JDH3_2