title: Hep-G2 cell, Electroporation control treatment, 24 hours, replicate 1

description: Library name: HepG2_ctrl_24h_rep1


title: M0-Exo-1

status: Public on Jan 23 2026

type: SRA

city: Lanzhou

first: Zhenchang

last: Zhang

state: Gansu

address: No. 222, Tianshui South Road

department: The Second Hospital & Clinical Medical School

country: China

institute: Lanzhou University

description:
Library name: Sample1
M0-Exo-1.norm

library_source: transcriptomic

data_processing:
Analysis workflow established on a local server v 1.1
Assembly: mm39
Supplementary files format and content: tab-delimited textfile includes CPMs for each Sample

molecule: total RNA

organism: Mus musculus

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen)
Small RNA libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Inc.) according to the manufacturer's instructions.

tag: cell line

tag: cell type

value: macrophage

tag: genotype

value: wild type

tag: treatment

tag: batch


title: Hep-G2 cell, HiFi FaDe Cas9 editing treatment, 24 hours, replicate 2

city: Mölndal

first: Benjamin

last: Keith

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

description: Library name: HepG2_KI_24h_rep2

data_processing:
Libraries were assessed using FastQC (v0.12.1), Qualimap (v2.2.2c) and SAMtools stats (v1.18). Alignment was performed using STAR (version 2.7.2b) with alignment against the human genome (GRCh38, Ensembl v105). Sequencing Quality control metrics were obtained using Qualimap (v2.2.2c) and summarized using MultiQC (v1.17). Trimming of adapters was performed using NGmerge (v0.3). A human transcriptome index consisting of cDNA and ncRNA entries from Ensembl v105) was generated and gene abundances were obtained using Salmon (v1.1.0). The bioinformatics workflow was organized using Nextflow workflow management system (v20.10) and Bioconda software management tool.
Differential gene expression analysis was performed using Dream (variancePartition v1.32.2). Gene set enrichment analysis was performed with FGSEA (v1.28.0) using Kyoto Encyclopedia of Genes and Genomes (KEGG; C2_CP:KEGG of the MSigDB collection v7.5.123). For plotting and data wrangling, Tidyverse (v2.0.0), PCAtools (v2.14.0) EnhancedVolcano (v1.18.0), and ComplexHeatmap (v2.18.024) were used. R 4.3.2 was used for downstream analyses.
Assembly: GRCh38, Ensembl 105
Supplementary files format and content: Raw counts from tximport, tab seprated
Supplementary files format and content: Transcripts per Million  counts from tximport abundances, tab separated

organism: Homo sapiens

source_name: liver

growth_protocol: MCF7 cells (ATCC HTB-22) were maintained in RPMI 1640 Medium, GlutaMAX, HEPES (Gibco #72400-047) with 10% FBS (Gibco #10270-106). HepG2 (ATCC HB-8065) were cultured in MEM, GlutaMAX (Gibco #41090-036) with 1x MEM non-essential amino acids solution (Gibco #11140-050), 1% (v/v) sodium pyruvate (Gibco #11360-070), and 10% FBS (Gibco #10270-106). Cell lines were regularly tested for mycoplasma contaminations, and cell identity was confirmed through STR profiling.

extract_protocol:
Total RNA was isolated from 5 × 10⁶ cells using a lysis buffer mix containing Proteinase K from the RNAdvance Tissue kit (Beckman Coulter). Cells were vortexed thoroughly and incubated at 37°C for 25 minutes. RNA isolation, including a 15-minute DNase I treatment, was carried out according to the manufacturer’s protocol on a Biomek i7 Hybrid robotic workstation (Beckman Coulter). RNA quantity and quality were assessed using a Fragment Analyzer 5300 system (Agilent), and RNA integrity number (RIN) values were recorded.
Total RNA-seq libraries were prepared using the KAPA RNA HyperPrep with RiboErase kit (Roche) on a Tecan Fluent® liquid handler, following the manufacturer’s instructions. Library integrity and quality were evaluated with the SS NGS Fragment Kit (1–6000 bp; Agilent) on a fragment analyzer. Sequencing was performed as paired-end 2 × 100 bp on an Illumina NovaSeq 6000 platform using a v1.5 SP Reagent kit (Illumina).

treatment_protocol: CRISPR reagents: For cell engineering purposes to specifically address precise KI efficiency, we used synthetic sgRNAs targeting SERPINA1 locus in combination with a single-strand DNA (HDR template) consisting of 39 nt to be integrated, flanked by 30 nt homology arms. Synthetic sgRNAs and HDR template were synthesized by Sigma-Aldrich, MERCK. Spacers and donor sequences are summarized in Table S1. The following small molecules were used in this study. PolQi1 (WO2021/028643, Example 158), PolQi2 (WO2020/243459, Example 99) were provided by AstraZeneca (Gothenburg, Sweden), and AZD7648 (HY-111783, MedChemExpress) is commercially available. All compounds were dissolved in DMSO (Sigma-Aldrich, MERCK #D2650) at a concentration of 10 mM. Transfections – RNP preparation and delivery: To prepare RNP complexes, spCas9-GFP (Sigma, MERCK #CAS9GFPPRO), sgRNAs, and ssDNA HDR template were incubated in a [1:1:1 molar ratio] for 10-15 min at room temperature. RNPs were kept on ice until electroporation. During RNP incubation, cells were washed with PBS (Gibco #10010023), detached with TrypLE Express Enzyme (Gibco #12604013), resuspended in cell culture medium, and cell number and viability were assessed using Nucleocounter NC-3000 cell counter (ChemoMetec). Prior to electroporation, cells were transferred into 15 ml tubes, washed with PBS and resuspended in Buffer R (Neon Transfection System, Invitrogen, #MPK1025) to a final density of 1 x 107 cells/ml. For electroporation, 5 x 105 cells (MCF7 or HepG2) were combined with 60 pmol spCas9 nuclease, 60pmol sgRNA (30pmol per guide), and 60pmol ssDNA. Electroporation was performed using Neon system (Invitrogen) applying the following settings: 1600V, 10ms pulse, 3 pulses. Afterwards, cells were transferred into 24-well plate format containing cell culture media with DMSO or small molecules at different concentrations (PolQi1 and PolQi2 at 1.5 µM, AZD7648 at 1µM). Transient transfections – plasmid delivery:  MCF7 cells were seeded into T75 flasks (60,000 cells/cm2) 24 hours before transfections. pMAZ-CMV-PCNA plasmid was transfected using Lipofectamine 3000 transfection reagent (Invitrogen, #L3000001) following manufacturer’s instructions. Briefly, a total of 8µg of plasmid DNA was used to transfect cells in T75 format. As positive control, the same number of cells were transfected in T75 flasks using pMAZ-CMV-EGFP, to address transfection efficiency and CMV promoter activity. Cells were cultured for 48h before the editing experiments.

tag: tissue

value: liver

value: Hep-G2 cell

value: epithelia

value: HiFi FaDe Cas9 editing

tag: treatment duration

value: 24 hours


title: MCF-7 cell, Electroporation control treatment, 24 hours, replicate 2

description: Library name: MCF7_ctrl_24h_rep2

source_name: breast

value: breast

value: MCF-7 cell

value: Electroporation control


title: Hep-G2 cell, HiFi FaDe Cas9 editing treatment, 48 hours, replicate 3

description: Library name: HepG2_KI_48h_rep3

value: 48 hours


title: 4_Inosine

city: Jinan

first: Fabao

last: Liu

state: Shandong

address: #44 wenhua xi road

institute: Shandong university

description: Library name: B_1

data_processing:
Sequencing reads were aligned to the Mus musculus genome (mm10) using HISAT2.
Duplicated reads and reads with low mapping quality were eliminated using Sambamba tools (v0.7.1). Feature Counts (subread package, v2.0.1) was used to count reads as a measure of gene expression. Differentially expressed genes were identified by DESeq2 (v1.38.3) in R.
Assembly: mm10
Supplementary files format and content: Differential_allgene.annot.results.txt

source_name: Primary cells

growth_protocol: All media were supplemented with 10% dialyzed fetal bovine serum (FBS).

extract_protocol:
The samples were sent to Bioyi Biotechnology Co., Ltd. (Wuhan, China) for RNA-seq.
Each library was sequenced in paired-end mode using the Illumina NovaSeq 6000 platforms.

treatment_protocol: 2mM glucose; 2mM inosine; 2mM inosine combined with 100 M hypoxanthine for 24h. Live cells (about 80%) were sorted by CytoFLEX SRT Cell Sorter (V5-B2-Y5-R0, Beckman)

value: CD8+ T cells

value: Inosine

value: Day 0


title: Hep-G2 cell, Electroporation control treatment, 48 hours, replicate 2

description: Library name: HepG2_ctrl_48h_rep2


title: 8_Inosine combined with hypoxanthine

description: Library name: C_2

value: Inosine combined with hypoxanthine


title: 5_Inosine

description: Library name: B_2


title: 7_Inosine combined with hypoxanthine

description: Library name: C_1


title: Late stage Col8a2 Q455K mutant corneal endothelium, replicate 3

city: Qingdao

first: Xintian

last: Zhao

address: shangma road,Qingdao,Shangdong,China

institute: Qingdao Eye Research Institute

description:
Library name: LSM_rep3
Col8a2 Q455K mutant mouse, late stage counts and expression data
gene_expression_late_mut_vs_wt.csv

data_processing:
Sequencing was performed on the Illumina Novaseq 6000 platform with 150 bp paired-end reads generated. Raw reads were quality-controlled using fastp software to remove adapter sequences and low-quality reads, resulting in clean reads. Clean reads were aligned to the mouse reference genome GRCm39 using HISAT2 software. Gene-level raw read counts were obtained by HTSeq-count. Differential expression analysis was conducted using DESeq2 software, which performs normalization and statistical testing based on a negative binomial distribution model to identify significantly differentially expressed genes.
Assembly: Mus musculus reference genome GRCm39
Supplementary files format and content: Processed data files consist of gene expression matrices in tab-delimited text format, including raw counts and normalized FPKM values, annotated with gene symbols and Ensembl gene IDs.

molecule: polyA RNA

source_name: corneal endothelium

extract_protocol:
Total RNA was extracted from tissues or cells using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions. RNA purity and concentration were assessed using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was evaluated with an Agilent 2100 Bioanalyzer (Agilent Technologies, USA) to ensure sample quality met the requirements for library construction.
RNA-seq libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (Cat. No. NEB#E7330S, NEB, USA) following the manufacturer’s instructions. The library preparation workflow included mRNA enrichment or rRNA depletion, RNA fragmentation, first- and second-strand cDNA synthesis with strand specificity, end repair, adapter ligation, and PCR amplification. Library quality and fragment size distribution were assessed using a Bioanalyzer to ensure suitability for sequencing.

value: corneal endothelium

tag: disease stage

value: Late stage

value: Col8a2 Q455K mutant


title: 2_Glucose

description: Library name: A_2

value: wild type

value: Glucose


title: EP300_KO_R1

city: Toronto

first: Fatemeh

last: Molaei

state: Ontario

address: 160 College St. Room 830, Terrence Donnelly Centre for Cellular & Biomolecular Research

country: Canada

institute: University of Toronto

description: Library name: EP300_KO_H3K27ac_R1

library_source: genomic

data_processing:
FASTQ files were aligned to the human genome (hg38) using Bowtie2 and  process them into Sam, Bam, bigwig and bedgraph files.
For peakCalling, we used SEACR (Sparse Enrichment Analysis for CUT&RUN) with cut off 0.01 for H3K27ac peak calls and 0.001 for P300 binding sites call.
Assembly: Homo sapiens hg38
Supplementary files format and content: Peak bed files are provided
Library strategy: CUT&Run

molecule: genomic DNA

source_name: Glioblastoma stem cell

extract_protocol:
Cells were fixed with 0.1% formaldyhe for 1 minute, then quench with  glycin at final concentration 125mM. CUT&RUN experiment and DNA extraction was done using the CUTANA ChIC/CUT&RUN kit (14-1048, EpiCypher).
Libraries were prepared using NEBNext Ultra II FS DNA library prep kit for illumina and quantified using the Qubit 1X dsDNA high sensitivity assay.

value: Glioblastoma stem cell


title: Late stage wild-type corneal endothelium, replicate 3

description:
Library name: LSWT_rep3
Wild-type mouse, late stage counts and expression data
gene_expression_late_mut_vs_wt.csv

value: Wild type


title: AAVS1_KO_R1

description: Library name: Control_H3K27ac-1


title: Hep-G2 cell, Electroporation control treatment, 24 hours, replicate 4

description: Library name: HepG2_ctrl_24h_rep4

value: liver

value: Hep-G2 cell

value: epithelia


title: EP300_KO_R3

description:
Library name: EP300_KO_R3
G549_RNA_counts.txt | EP300_R3

data_processing:
FASTQ files were aligned to the human transcriptome (hg37_cDNA) using Kallisto
Read counts were extracted and normalized using DESeq2
Assembly: Homo_sapiens.GRCh37.87
Supplementary files format and content: tab delimited text file containing DESeq2 normalized counts for each sample

extract_protocol:
RNA was extracted using the Trizol reagent (invitrogen).
RNA-seq libraries (4 biological replicates each sample) were derived using NEBNext Poly(A) mRNA Magnetic isolation module followed by NEBNext Ultra II Directional RNA library prep kit.


title: Early stage Col8a2 Q455K mutant corneal endothelium, replicate 3

description:
Library name: ESM_rep3
Col8a2 Q455K mutant mouse, early stage counts and expression data
gene_expression_early_mut_vs_wt.csv

value: Early stage


title: EP300_KO_R2

description:
Library name: EP300_KO_R2
G549_RNA_counts.txt | EP300_R2


title: Late stage wild-type corneal endothelium, replicate 2

description:
Library name: LSWT_rep2
Wild-type mouse, late stage counts and expression data
gene_expression_late_mut_vs_wt.csv


title: Late stage wild-type corneal endothelium, replicate 1

description:
Library name: LSWT_rep1
Wild-type mouse, late stage counts and expression data
gene_expression_late_mut_vs_wt.csv


title: Hep-G2 cell, Electroporation control treatment, 24 hours, replicate 2

description: Library name: HepG2_ctrl_24h_rep2

value: Electroporation control

value: 24 hours


title: WT_P300binding_R1

description: Library name: WT-p300-1

value: WT


title: WT_P300binding_R2

description: Library name: WT-p300-2


title: Late stage Col8a2 Q455K mutant corneal endothelium, replicate 2

description:
Library name: LSM_rep2
Col8a2 Q455K mutant mouse, late stage counts and expression data
gene_expression_late_mut_vs_wt.csv


title: 1_Glucose

description: Library name: A_1

value: CD8+ T cells


title: Mx1-Elk1_MatN_replicate2

city: chengdu

first: Yong

last: Dong

state: sichuan

address: Xindu road 783, Xindu district

department: Immunology

institute: Chengdu medical college

description: Library name: Sample38

data_processing:
For single cell RNA sequencing analysis, all fastq files are mapped to mouse mm10 genome to generate gene expression matrix by Cell Ranger 4.0.4 software.  For bulk-cell RNA sequencing analysis, all fastq files are mapped to mouse mm10 genome by hist2 software to generate the bam files, and then featurecount software is used to generate the gene expression raw count matrix, and the raw data matirx converted into CMP (count per million) value matirx.
Assembly: mouse mm10
Supplementary files format and content: Filtered_feature_bc_matrix.rar for single cell RNA sequencing samples
Supplementary files format and content: bulk_cell_cpm_normalized_data.csv file containing the CMP value for all bulk-cell RNA sequencing samples

source_name: Mx1-Elk1 transgenic mouse

extract_protocol:
For single cell RNAseq, CD3/CD19/NK1.1/Ter119－ CD11b+ and CD3/CD19/NK1.1/Ter119－C-kit+ cells derived from Mx1-Elk1 and littermate control mice are sorted and these two cell populations are mixed together at the ratio 1:2. For bulk-cell RNAseq,  LSK, CMP, GMP, MEP, immature neutrophils and mature neutrophils derived from  Mx1-Elk1 and littermate control mice were sorted and collected with PCR tube with 0.5%BSA-PBS buffer. 3000 cells of each population were used for each sample.
For single cell RNA sequenceing, sorted cells are harvested by 10X Genomics Chromium system, then single cell libraries are generated by this system. RNA sequencing are perfomed by NovaSeq X plus system (library construction and sequencing of single cell were performed by HaploX company)..  For bulk-cell RNA sequence, all transcripts were converted into dsDNA for each population were generated according to previous reported procedures (Dong, Y., et al., Cells, 2019. 8(9), Tang, F., et al., Nat. Protoc. 2010, 5, 516–535.). Libraries were constructed by TruePrep DNA Library Prep Kit V2 for Illumina (TD503, Vazyme, Co.Ltd) and all the libraries were sequenced using the Illumina NovaSeq X plus system (HaploX company. Ltd.).

value: Bone marrow

value: Sorted mature neutrophils cells


title: EP300_KO_R4

description:
Library name: EP300_KO_R4
G549_RNA_counts.txt | EP300_R4


title: AAVS1_KO_R2

description: Library name: Control-H3K27ac-2


title: EP300_KO_R2

description: Library name: EP300_KO_H3K27ac_R2


title: POI, rep31

city: Hangzhou

first: Yifei

last: Lv

address: 1 Xueshi Rd, Hangzhou, People’s Republic of China

institute: Women’s Hospital, Zhejiang University School of Medicine

description: Library name: POI_31

data_processing:
Differential gene expression was analyzed with the edgeR R package, including 32 patients with POI and 30 controls. P-values were adjusted using the Benjamini-Hochberg method. Student’s t-test was used to evaluate significance.
Assembly: mm39
Supplementary files format and content: gene_count.xls includes raw counts for each Sample
Supplementary files format and content: gene_fpkm.xls includes FPKM values for each Sample

source_name: peripheral blood mononuclear cells

extract_protocol:
Total RNA was isolated from PBMCs using RNAiso Plus (Takara, Japan). mRNA was purified with poly T oligo-attached magnetic beads to establish cDNA libraries for RNA sequencing. Library fragments (370–420 bp) were purified using the AMPure XP System (Beckman Coulter, Beverly, USA). The cDNA library quality was assessed using the Agilent Bioanalyzer 2100 system.
Paired-end sequencing (150 bp) was performed on an Illumina NovaSeq platform. Transcriptomic mapping and profiling were conducted by Novogene (Beijing, China).

treatment_protocol: Peripheral blood samples were obtained from women diagnosed with POI at Gynecological Endocrinology outpatient clinics and from women without ovarian disorders identified through physical examinations. POI was defined as oligo/amenorrhea for at least 4 months in women under 40 years, and an increased follicle-stimulating hormone serum concentration >25 IU/L detected on at least two separate occasions >4 weeks apart. Total RNA was isolated from PBMCs within 1 hour of collection and stored.

value: peripheral blood mononuclear cells


title: Early stage wild-type corneal endothelium, replicate 2

description:
Library name: ESWT_rep2
Wild-type mouse, early stage counts and expression data
gene_expression_early_mut_vs_wt.csv

value: corneal endothelium


title: Late stage Col8a2 Q455K mutant corneal endothelium, replicate 1

description:
Library name: LSM_rep1
Col8a2 Q455K mutant mouse, late stage counts and expression data
gene_expression_late_mut_vs_wt.csv

value: Late stage

value: Col8a2 Q455K mutant


title: Early stage wild-type corneal endothelium, replicate 1

description:
Library name: ESWT_rep1
Wild-type mouse, early stage counts and expression data
gene_expression_early_mut_vs_wt.csv


title: Early stage wild-type corneal endothelium, replicate 3

description:
Library name: ESWT_rep3
Wild-type mouse, early stage counts and expression data
gene_expression_early_mut_vs_wt.csv


title: EP300_KO_R1

description:
Library name: EP300_KO_R1
G549_RNA_counts.txt | EP300_R1


title: POI, rep30

description: Library name: POI_30


title: Early stage Col8a2 Q455K mutant corneal endothelium, replicate 2

description:
Library name: ESM_rep2
Col8a2 Q455K mutant mouse, early stage counts and expression data
gene_expression_early_mut_vs_wt.csv


title: Mx1-Elk1_MEP_replicate2

description: Library name: Sample32

value: Sorted MEP cells


title: Mx1-Elk1_MatN_replicate3

description: Library name: Sample39


title: Early stage Col8a2 Q455K mutant corneal endothelium, replicate 1

description:
Library name: ESM_rep1
Col8a2 Q455K mutant mouse, early stage counts and expression data
gene_expression_early_mut_vs_wt.csv


title: AAVS1_KO_R4

description:
Library name: Control-4
G549_RNA_counts.txt | AAVS1_R4

value: Glioblastoma stem cell


title: AAVS1_KO_R2

description:
Library name: Control-2
G549_RNA_counts.txt | AAVS1_R2


title: AAVS1_KO_R1

description:
Library name: Control-1
G549_RNA_counts.txt | AAVS1_R1


title: Mx1-Elk1_MEP_replicate1

description: Library name: Sample31


title: POI, rep32

description: Library name: POI_32


title: Mx1-Elk1_MatN_replicate1

description: Library name: Sample37


title: AAVS1_KO_R3

description:
Library name: Control-3
G549_RNA_counts.txt | AAVS1_R3


title: Mx1-Elk1_ImmN_replicate1

description: Library name: Sample34

value: Sorted immature neutrophils cells


title: POI, rep26

description: Library name: POI_26


title: Mx1-Elk1_ImmN_replicate3

description: Library name: Sample36


title: Mx1-Elk1_MEP_replicate3

description: Library name: Sample33


title: Mx1-Elk1_GMP_replicate3

description: Library name: Sample30

value: Sorted GMP cells


title: POI, rep28

description: Library name: POI_28


title: POI, rep29

description: Library name: POI_29


title: Mx1-Elk1_GMP_replicate1

description: Library name: Sample28


title: POI, rep27

description: Library name: POI_27


title: POI, rep24

description: Library name: POI_24


title: Mx1-Elk1_ImmN_replicate2

description: Library name: Sample35


title: POI, rep23

description: Library name: POI_23


title: POI, rep25

description: Library name: POI_25


title: Mx1-Elk1_CMP_replicate3

description: Library name: Sample27

value: Sorted CMP cells


title: POI, rep21

description: Library name: POI_21


title: POI, rep22

description: Library name: POI_22


title: Mx1-Elk1_CMP_replicate2

description: Library name: Sample26


title: Mx1-Elk1_CMP_replicate1

description: Library name: Sample25


title: Mx1-Elk1_LSK_replicate2

description: Library name: Sample23

value: Sorted LSK cells


title: POI, rep19

description: Library name: POI_19


title: POI, rep20

description: Library name: POI_20


title: Mx1-Elk1_LSK_replicate3

description: Library name: Sample24


title: POI, rep17

description: Library name: POI_17


title: POI, rep18

description: Library name: POI_18


title: Small RNAs from UAS-GFP-antisenseTirant driven by traffic jam Gal4 - replicate 2

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

description:
Library name: UAS-GFP-antisenseTirant_rep2
sRNA_counts_Tirant.txt.gz
pBA79_rep2

library_source: other

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (TACCA AGATCGGAAGAGCACACGTCT)
Adapter clipped reads were trimmed by 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
Reads were mapped to the Drosophila melanogaster dm6 genome and a curated TE consensus sequence file using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
Reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
Reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6 + TE consensus sequences (in-house curated list of TE sequences)
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: Table with sRNA counts quantified on TE-sequences per strand. Numbers calculated as Reads per kb TE per 1 million miRNAs
Supplementary files format and content: Curated TE-consensus file used for the TE quantification analysis

molecule: other

organism: Drosophila melanogaster

source_name: Ovary

growth_protocol: 25˚C, 12h dark/light, ovaries dissected into PBS on ice, snap frozen

extract_protocol:
Argonaute-bound sRNAs were isolated using TraPR columns according to Grentzinger et al. (2020)
Libraries were prepared by ligation of 3' barcoded adaptors containing 6 random nucleotides and a 5 nt in-line barcode and 5' adaptors containing 4 random nucleotides at the ends to reduce ligation biases followed by reverse transcription and amplification by PCR.

value: Ovary


title: Small RNAs from UAS-GFP-antisenseTirant driven by traffic jam Gal4 - replicate 1

description:
Library name: UAS-GFP-antisenseTirant_rep1
sRNA_counts_Tirant.txt.gz
pBA79_rep1

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (GGTAT AGATCGGAAGAGCACACGTCT)
Adapter clipped reads were trimmed by 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
Reads were mapped to the Drosophila melanogaster dm6 genome and a curated TE consensus sequence file using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
Reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
Reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6 + TE consensus sequences (in-house curated list of TE sequences)
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: Table with sRNA counts quantified on TE-sequences per strand. Numbers calculated as Reads per kb TE per 1 million miRNAs
Supplementary files format and content: Curated TE-consensus file used for the TE quantification analysis


title: Ctrl_MatN_replicate2

description: Library name: Sample20

source_name: C57/BL6 wild type mouse


title: Small RNAs from UAS-GFP-senseTirant driven by traffic jam Gal4 - replicate 1

description:
Library name: UAS-GFP-senseTirant_rep1
sRNA_counts_Tirant.txt.gz
pBA80_rep1

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (GTCAG AGATCGGAAGAGCACACGTCT)
Adapter clipped reads were trimmed by 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
Reads were mapped to the Drosophila melanogaster dm6 genome and a curated TE consensus sequence file using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
Reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
Reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6 + TE consensus sequences (in-house curated list of TE sequences)
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: Table with sRNA counts quantified on TE-sequences per strand. Numbers calculated as Reads per kb TE per 1 million miRNAs
Supplementary files format and content: Curated TE-consensus file used for the TE quantification analysis


title: Ctrl_MatN_replicate3

description: Library name: Sample21


title: POI, rep15

description: Library name: POI_15


title: Ctrl_MatN_replicate1

description: Library name: Sample19


title: POI, rep16

description: Library name: POI_16


title: Ctrl_ImmN_replicate3

description: Library name: Sample18


title: FCH_1

city: Tianjin

first: Jingxu

last: Duan

institute: Tianjin university

description: Library name: sample 13

data_processing:
Therawpairedendreadsweretrimmedandqualitycontrolledbyfastp withdefaultparameters.Thenclean readswereseparatelyalignedtoreferencegenomewithorientationmodeusingHISAT2 software.Themapped readsofeachsamplewereassembledbyStringTie inareference-basedapproach.
Assembly: http://www.ensembl.org/Homo sapiens/Info/Index
Supplementary files format and content: It is a tab-delimited text file compressed using gzip. It contains a gene expression matrix, where rows represent genes (identified by Gene_Symbol), and columns represent samples (including NC, FFA, FCL, FCM, and FCH groups, as well as their biological replicates). The values in the matrix represent gene expression levels after log2(FPKM+1) transformation. This file can be directly used for downstream differential expression and functional enrichment analyses.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according to the manufacturer's instructions. RNA quality was assessed using a 5300 Bioanalyzer (Agilent) and quantified with an ND-2000 (NanoDrop Technologies). Only high-quality RNA samples [Concentration ≥ 20 ng/μL, total RNA > 1 μg, RQN > 4.5] were used for sequencing library construction.
RNApurification, reverse transcription, library construction and sequencingwereperformed at Shanghai MajorbioBio-pharmBiotechnologyCo.,Ltd. (Shanghai,China)accordingtothemanufacturer’sinstructions.The XXRNA-seqtranscriptomelibrariywaspreparedfollowingIllumina®StrandedmRNAPrep,Ligation(SanDiego, CA) using1μgof totalRNA. Shortly,messengerRNAwas isolatedaccording topolyAselectionmethodby oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNAwas synthesized with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylationandadapteradditionaccordingtolibraryconstructionprotocol.Librariesweresizeselectedfor cDNAtarget fragmentsof300-400bpusemagneticbeadsfollowedbyPCRamplifiedfor10-15PCRcycles.

value: liver

value: hepatocyte


title: Mx1-Elk1_GMP_replicate2

description: Library name: Sample29


title: Mx1-Elk1_LSK_replicate1

description: Library name: Sample22


title: FCM_3

description: Library name: sample 12


title: POI, rep14

description: Library name: POI_14


title: Ctrl_ImmN_replicate1

description: Library name: Sample16


title: FCM_1

description: Library name: sample 10


title: Small RNAs from UAS-GFP-senseTirant driven by traffic jam Gal4 - replicate 2

description:
Library name: UAS-GFP-senseTirant_rep2
sRNA_counts_Tirant.txt.gz
pBA80_rep2

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (TGACT AGATCGGAAGAGCACACGTCT)
Adapter clipped reads were trimmed by 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
Reads were mapped to the Drosophila melanogaster dm6 genome and a curated TE consensus sequence file using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
Reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
Reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6 + TE consensus sequences (in-house curated list of TE sequences)
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: Table with sRNA counts quantified on TE-sequences per strand. Numbers calculated as Reads per kb TE per 1 million miRNAs
Supplementary files format and content: Curated TE-consensus file used for the TE quantification analysis


title: POI, rep12

description: Library name: POI_12


title: POI, rep13

description: Library name: POI_13


title: FCM_2

description: Library name: sample 11


title: FCL_3

description: Library name: sample 9


title: Ctrl_ImmN_replicate2

description: Library name: Sample17


title: FCH_3

description: Library name: sample 15


title: FFA_2

description: Library name: sample 5


title: Ctrl_MEP_replicate3

description: Library name: Sample15


title: FCL_1

description: Library name: sample 7


title: FCH_2

description: Library name: sample 14


title: FCL_2

description: Library name: sample 8


title: POI, rep10

description: Library name: POI_10


title: FFA_3

description: Library name: sample 6


title: POI, rep11

description: Library name: POI_11


title: NC_2

description: Library name: sample 2


title: FFA_1

description: Library name: sample 4


title: POI, rep9

description: Library name: POI_9


title: POI, rep8

description: Library name: POI_8


title: PBMC_sample15_Patient290

city: BETHESDA

first: Cihan

last: Oguz

state: MD

address: NIHBC 29B BG RM 1NN20, 9000 ROCKVILLE PIKE

country: USA

institute: NIH

description: Library name: 5435

library_source: transcriptomic single cell

data_processing:
Raw scRNA-Seq data derived from 10x Genomics Single Cell Chromium 3' v3 mRNA libraries were processed using Cell Ranger v7.1.0  run with default parameter settings and the GRCh38-2020-A transcriptome reference to generate the counts in the filtered_feature_bc_matrix.h5 files.
Assembly: hg38 (Cell Ranger GRCh38-2020-A reference). Human GRCh38 (GENCODE v32/Ensembl98): https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-reference-release-notes)
Supplementary files format and content: Cell Ranger scRNA-seq count matrices are in the h5 data format (one h5 file per sample).

source_name: PBMC

extract_protocol:
RNA was extracted from cryopreserved ficoll-isolated peripheral blood mononuclear cells (PBMCs).
Single-cell RNA-sequencing libraries were prepared using the Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 (10X Genomics) and processed on the Chromium X System (10X Genomics), according to manufacturer’s protocol.

value: PBMC

value: LATE ACUTE


title: Ctrl_GMP_replicate3

description: Library name: Sample12

value: Bone marrow


title: Ctrl_GMP_replicate2

description: Library name: Sample11


title: PBMC_sample13_Patient297

description: Library name: 5433

value: EARLY ACUTE


title: POI, rep7

description: Library name: POI_7

value: peripheral blood mononuclear cells


title: POI, rep6

description: Library name: POI_6


title: PBMC_sample12_Patient281

description: Library name: 5432

value: REBOUND


title: Ctrl_GMP_replicate1

description: Library name: Sample10


title: PBMC_sample14_Patient296

description: Library name: 5434


title: PBMC_sample10_Patient289

description: Library name: 5430


title: Ctrl_MEP_replicate2

description: Library name: Sample14


title: POI, rep5

description: Library name: POI_5


title: NC_1

description: Library name: sample 1


title: Ctrl_CMP_replicate2

description: Library name: Sample8


title: PBMC_sample11_Patient283

description: Library name: 5431


title: Ctrl_MEP_replicate1

description: Library name: Sample13


title: PBMC_sample9_Patient286

description: Library name: 5429


title: NC_3

description: Library name: sample 3


title: POI, rep3

description: Library name: POI_3


title: PBMC_sample5_Patient281

description: Library name: 5425


title: PBMC_sample8_Patient284

description: Library name: 5428


title: Ctrl_CMP_replicate1

description: Library name: Sample7


title: PBMC_sample7_Patient283

description: Library name: 5427


title: Ctrl_CMP_replicate3

description: Library name: Sample9


title: Ctrl_LSK_replicate3

description: Library name: Sample6

value: Sorted Lin-Sca1+cKit+ (LSK) cells


title: PBMC_sample6_Patient282

description: Library name: 5426


title: PBMC_sample3_Patient275

description: Library name: 5423


title: PBMC_sample4_Patient279

description: Library name: 5424


title: POI, rep4

description: Library name: POI_4


title: POI, rep2

description: Library name: POI_2


title: POI, rep1

description: Library name: POI_1


title: Ctrl_LSK_replicate2

description: Library name: Sample5

value: Sorted Lin-Sca1+cKit+ (LSK)  cells


title: PBMC_sample2_Patient274

description: Library name: 5422


title: PBMC_sample1_Patient258

description: Library name: 5421


title: IUGR/B6I5_PLA(raw)

city: Aurora

first: JAMES

middle: R

last: BARDILL

state: CO

department: Surgery

institute: UNIVERSITY OF COLORADO-ANSCHUTZ MED

description:
Library name: Sample 20
column name in Table8.1_IUGRvsControl_GEO submission.txt:  IUGR/B6I5_PLA(raw)

data_processing:
The ACGT101-miR program removed adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA), and repeats.
Unique sequences (18–26 nucleotides) were mapped to species-specific precursors in miRBase 22.0 by BLAST search to identify known and novel 3p- and 5p-derived miRNAs. Sequences mapping to mature miRNAs in hairpin arms were identified as known miRNAs, while those mapping to the opposite arm of known precursors were novel candidates. Remaining sequences were mapped to other selected species’ precursors in miRBase 22.0 and further BLASTed against the Homo sapiens genome to determine their genomic locations.
Assembly: mm39, miRBase
Supplementary files format and content: Raw miRNA counts
Supplementary files format and content: Table8.1_IUGRvsControl_GEO submission.txt

source_name: Placenta

growth_protocol: Pregnant C57BL/6 mice were provided ad libitum access to food between E1-E8.5. Beginning at E8.5 and continuing until tissue harvest, pregnant dams were divided into two groups as previously described.  Control dams continued to have ad libitum access to food.

extract_protocol:
Total RNA was extracted from mouse placenta samples (with intact decidua layer) using a bead homogenizer and Trizol LS reagent (ThermoFisher, 10-296-028) /chloroform method. RNA concentration was measured using the NanoDrop 2000c spectrophotometer (Thermofisher Scientific). If necessary, an RNA clean and concentrator kit (Zymo Research R1019) was used to remove any contaminating DNA, phenol, and concentrate samples to improve 260/280 (1.9-2.0) and 260/230 ratios (2.0-2.2).
Sequencing was performed by LC Sciences (Houston, Texas, USA). We used 1 µg of total RNA to prepare small RNA libraries with TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA). Single-end 50bp sequencing was conducted on an Illumina Hiseq 2500 system.

treatment_protocol: The IUGR (FGR) group received a 50% caloric restricted diet, which was calculated from a predetermined average ad libitum intake. This caloric restriction equated to approximately 1.5-2.0 grams of food provided daily

value: Placenta

value: IUGR


title: Elane-Elk1

description: Library name: Sample3

source_name: Elane-Elk1 transgenic mouse

value: Sorted myeloid cells and hematopoietic stem and progeintors cells


title: Mx1-Elk1

description: Library name: Sample2


title: IUGR/B6I1_PLA(raw)

description:
Library name: Sample 16
column name in Table8.1_IUGRvsControl_GEO submission.txt:  IUGR/B6I1_PLA(raw)


title: Control, rep30

description: Library name: CT_30


title: IUGR/B69F_PLA(raw)

description:
Library name: Sample 15
column name in Table8.1_IUGRvsControl_GEO submission.txt:  IUGR/B69F_PLA(raw)


title: WT

description: Library name: Sample1

source_name: C57/BL6 litermate control  mouse


title: Control, rep29

description: Library name: CT_29


title: Control, rep28

description: Library name: CT_28


title: IUGR/B610F_PLA(raw)

description:
Library name: Sample 11
column name in Table8.1_IUGRvsControl_GEO submission.txt:  IUGR/B610F_PLA(raw)


title: Control, rep26

description: Library name: CT_26


title: IUGR/B611F_PLA(raw)

description:
Library name: Sample 12
column name in Table8.1_IUGRvsControl_GEO submission.txt:  IUGR/B611F_PLA(raw)


title: IUGR/B6I3_PLA(raw)

description:
Library name: Sample 18
column name in Table8.1_IUGRvsControl_GEO submission.txt:  IUGR/B6I3_PLA(raw)


title: IUGR/B6I4_PLA(raw)

description:
Library name: Sample 19
column name in Table8.1_IUGRvsControl_GEO submission.txt:  IUGR/B6I4_PLA(raw)


title: IUGR/B68F_PLA(raw)

description:
Library name: Sample 14
column name in Table8.1_IUGRvsControl_GEO submission.txt:  IUGR/B68F_PLA(raw)


title: PRDM16cKO snRNA-seq

city: New York

first: Wei

last: Wang

state: New York

address: 1230 York Ave.

department: Bioinformatics Resource Center

institute: The Rockefeller University

description:
Library name: PRDM16cKO
10X Genomics

data_processing:
the demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v6.1.2
Assembly: mm10 genome (v2020)
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: msenteric perivascular adipose tissue

extract_protocol:
Mesenteric perivascular adipose tissue was microdissected from mice and snap-frozen in liquid nitrogen. Snap-frozen fat pads were homogenized in TST buffer (146 mM NaCl, 21 mM MgCl2, 10 mM Tris-HCl pH7.5, 1 mM CaCl2, 1% Molecular Grade BSA, 0.2 U/µL RNase inhibitor, 0.1% Tween-20, in Ultrapure H2O) using a GentleMACS Tissue Dissociator. Homogenized tissues were then centrifuged. Pellets that contained nuclei were collected and further purified with an iodixanol gradient.
snRNAseq library was prepared using 10x Chromium Next GEM Single Cell 3’ kit v3.1 16 rxns (PN-1000268), following the manufacturer’s protocol.

value: msenteric perivascular adipose tissue

tag: age

value: Prdm16flox, AdopiQCre+


title: Control/B6C9_PLA(raw)

description:
Library name: Sample 10
column name in Table8.1_IUGRvsControl_GEO submission.txt:  Control/B6C9_PLA(raw)

value: Control


title: Ctrl_LSK_replicate1

description: Library name: Sample4


title: IUGR/B67F_PLA(raw)

description:
Library name: Sample 13
column name in Table8.1_IUGRvsControl_GEO submission.txt:  IUGR/B67F_PLA(raw)


title: Control/B6C8_PLA(raw)

description:
Library name: Sample 9
column name in Table8.1_IUGRvsControl_GEO submission.txt:  Control/B6C8_PLA(raw)


title: FoxP control, rep4

city: Nijmegen

first: Nicholas

last: Raun

address: Geert Grooteplein 10

country: Netherlands

institute: Radboudumc

description: Library name: Control-4

data_processing:
Sequenced reads were aligned with Burrows-Wheeler algorithm to the Drosophila reference genome with gene annotations extracted from the file Drosophila_melanogaster.BDGP5.77.gtf, available at http://www.ensembl.org (BDGP.5, http://www.fruitfly.org/) allowing one mismatch. Read counts were generated per gene with Rsubread v1.16.1. Only tags that were uniquely aligned to the genome were considered for further analysis.
Assembly: BDGP.5
Supplementary files format and content: wiggle file for visualization in genome browser

source_name: Whole brain

extract_protocol:
Twelve brains of freshly eclosed males per sample were dissected in PBS at ZT1-2, transferred to RNAIater solution (Sigma), and immediately frozen in liquid nitrogen. Total RNA was extracted using the Arcturus PicoPure RNA Purification kit (Thermo Fisher Scientific).
TruSeq RNA Sample Preparation Kit (Illumina) was used to prepare adapter ligated PCR fragments for sequencing. mRNA was purified using polyA selection and was reverse transcribed into a single-stranded cDNA using random hexamer priming. Second strand synthesis was performed to create double-stranded cDNA. The cDNA was then summited to DNA end repair with adenylation followed by ligation of Illumina sequencing adaptors and size selection for 300 bp. Fragments were amplified linearly with 14 PCR cycles and the sample quality of the fragments was validated using the 2100 Agilent Bioanalyzer.

value: Whole brain

value: FoxP control

tag: Sex

value: male


title: HGP_IP

city: Nanjing

first: Xirui

last: Li

address: #101 Longmian Avenue, Jiangning District

institute: Nanjing Medical University

description: Library name: sample4

data_processing:
Raw sequencing data were filtered by Trimmomatic v 0.36
The clean reads were mapped using STRA software v 2.5.3a
The reads distribution were analyed using RSeQO v 2.6
The peak was calling using MACS2 v 2.1.1
The peaks were annotate and distribute using bedtools v 2.25.0
The GO and KEGG analysis for differentially bindings peaks were implemented by KOBAS software v 2.1.1
Assembly: GRCm39_release109
Supplementary files format and content: bigWig,narrowReaks(except for input sample)

source_name: islet beta cell

growth_protocol: MIN6 cells were cultured  in DMEM with 15% FBS, 10mmol/l HEPES, 1mmol/l sodium pyruvate, 100 units/ml penicillin, 100 mg/ml streptavidin, and 50 mmol/l β-mercaptoethanol

extract_protocol:
Cells were fixed in 1% formaldehyde for 15 min,after quenching and cell lysis,chromatin was sonicated using a Sonics VCS130
The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3, the 10% DNA was used as starting material for input and 80% for IP samples. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Illumina Novaseq 6000 with PE150 model.

treatment_protocol: Cells were cultured in a modified medium containing 0.5% (w:v) BSA,  high glucose 33.3 mmol/l  and palmitate 0.4 mmol/l

value: islet beta cell

value: high glucose and palmitate


title: Control, rep24

description: Library name: CT_24


title: wt snRNA-seq

description:
Library name: wt
10X Genomics


title: HGP_input

description: Library name: sample3


title: Control, rep23

description: Library name: CT_23


title: Control, rep25

description: Library name: CT_25


title: Control/B6C15_PLA(raw)

description:
Library name: Sample 8
column name in Table8.1_IUGRvsControl_GEO submission.txt:  Control/B6C15_PLA(raw)


title: IUGR/B6I2_PLA(raw)

description:
Library name: Sample 17
column name in Table8.1_IUGRvsControl_GEO submission.txt:  IUGR/B6I2_PLA(raw)


title: FoxP control, rep3

description: Library name: Control-3


title: Control, rep27

description: Library name: CT_27


title: NGP_IP

description: Library name: sample2

value: nomal


title: Control, rep22

description: Library name: CT_22


title: FoxP control, rep2

description: Library name: Control-2


title: Control/B6C13_PLA(raw)

description:
Library name: Sample 7
column name in Table8.1_IUGRvsControl_GEO submission.txt:  Control/B6C13_PLA(raw)


title: NGP_input

description: Library name: sample1


title: Control/B6C10_PLA(raw)

description:
Library name: Sample 6
column name in Table8.1_IUGRvsControl_GEO submission.txt:  Control/B6C10_PLA(raw)


title: HGP

description: Library name: sample2

data_processing:
Raw sequencing data was filtered by Trimmomatic v 0.36
Clean data were mapped using STRA software v 2.5.3a
Genes differentially expressed between groups were identified using the edgeR package v 3.12.1.
Gene GO and KEGG analysis for differentially expressed gene were implemented by KOBAS software v 2.1.1
Alternative splicing events were detecten by using rMATS v 3.2.5
Assembly: GRCm39_release109
Supplementary files format and content: tab-delimited tex file includes raw counts for each Sample

extract_protocol:
RNA were extracted using Trizol reagent. A total amount of 1 μg RNA per sample was used for library construction.
RNA libraries for RNA-seq were prepared using KCTM Stranded mRNA Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: Cells were cultured in a modified medium containing 0.5% (w:v) BSA,  high glucose 33.3 mmol/l  and palmitate 0.4 mmol/l.


title: Control/B66F_PLA(raw)

description:
Library name: Sample 5
column name in Table8.1_IUGRvsControl_GEO submission.txt:  Control/B66F_PLA(raw)


title: FoxP mutant, rep3

description: Library name: FoxP-3

value: FoxP mutant


title: Control, rep20

description: Library name: CT_20

value: peripheral blood mononuclear cells


title: FoxP mutant, rep4

description: Library name: FoxP-4


title: Control/B64F_PLA(raw)

description:
Library name: Sample 4
column name in Table8.1_IUGRvsControl_GEO submission.txt:  Control/B64F_PLA(raw)


title: NGP

description: Library name: sample1


title: FoxP control, rep1

description: Library name: Control-1


title: adBNST, male, CVMS, rep4

city: New Brunswick

first: Thomas

middle: J

last: Degroat

state: NJ

address: 10 Suydam Street, Apt 12

department: Animal Sciences

institute: Rutgers University

data_processing:
Reads were quality trimmed with the FastX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) with a minimum quality score of 20.0.
Reads were then aligned to the mm10 reference genome using STAR and the NCBI RefSeq mm10 gene annotation.
Reads were counted with FeatureCounts.
Assembly: mm10
Supplementary files format and content: comma separated variable file with raw counts for each sample

source_name: neuro, adBNST

extract_protocol:
Mice were first anaesthetized via ketamine followed by decapitation. Brains were dissected out, sliced, and then microdissected to isolate the adBNST. Tissue samples from 3 biological replicates were then pooled prior to RNA extraction and were stored in RNAlater at -80°C. RNA was extracted using an RNAqueous Micro Isolation kit (Invitrogen; AM1931). Integrity, concentration, and quality of the RNA samples were analyzed with an Agilent 2100 Bioanalyzer.
Libraries were constructed using Illumina TruSeq Stranded mRNA Library Prep Kit with KAPA HiFi HotStart Ready Mix for the final PCR step

treatment_protocol: The Chronic Variable Mild Stress (CVMS) paradigm is 6-week schedule of 1-2 minor stressors every day, typically with one morning stressor and one evening stressor. Stressors include: 3 or 8 hours of humid bedding, 8 hours of no bedding, 8 hours of replacing bedding with room temperature water, placing the cage on a 45° tilt for 8 hours, isolation for 8 hours or overnight, exposure to novel mice’s dirty cages for 8 hours, lights on overnight, 2 or 3 hours of dark during typical light cycle, 5 or 6 bedding changes in a single day, 2 minute swim stress in 4°C water, 4 minute swim stress in room temperature water, 15 minute cold stress, 15 minutes of predator sounds, and 1 hour of restraint stress. These stressors were randomized throughout the 6 weeks.

value: neuro, adBNST

value: stressed


title: FoxP mutant, rep1

description: Library name: FoxP-1


title: adBNST, male, CVMS, rep5


title: FoxP mutant, rep2

description: Library name: FoxP-2


title: Control/B62F_PLA(raw)

description:
Library name: Sample 2
column name in Table8.1_IUGRvsControl_GEO submission.txt:  Control/B62F_PLA(raw)


title: adBNST, male, CVMS, rep3


title: Control, rep19

description: Library name: CT_19


title: Control/B63F_PLA(raw)

description:
Library name: Sample 3
column name in Table8.1_IUGRvsControl_GEO submission.txt:  Control/B63F_PLA(raw)


title: Control, rep18

description: Library name: CT_18


title: KPO2-rep2_ATAC

city: Gothenburg

first: Volkan

last: Sayin

address: Medicinaregatan 1F

department: Department of Surgery

institute: University of Gothenburg

data_processing:
Sequencing adapters and low-quality bases are trimmed using Trimmomatic 0.38
MACS2 2.1.2 was used for peak calling to identify open chromatin region
Assembly: mm10
Supplementary files format and content: bigWig

source_name: primary lung tumor

extract_protocol:
cell suspensions of 500,000 cells were sent for further processing to an external facility at  Genewiz (Azenta).
Samples were further processed by 150-bp-paired-end sequencing on an Illumina HiSeq 2500 at the external facility

value: primary lung tumor

value: KP-O

value: epithelial cells

value: KrasG12D; p53 fl/fl


title: Control, rep17

description: Library name: CT_17


title: Control, rep21

description: Library name: CT_21


title: Control/B61F_PLA(raw)

description:
Library name: Sample 1
column name in Table8.1_IUGRvsControl_GEO submission.txt:  Control/B61F_PLA(raw)

value: Placenta


title: Control, rep16

description: Library name: CT_16


title: adBNST, male, CVMS, rep2


title: KPO2-rep1_ATAC


title: KO iPSCs derived NPCs, bio rep3

city: La Jolla

first: FANG

last: YUAN

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys

data_processing:
QC were performed with Fastqc. Then Salmon were used to assign sequencing reads to transcripts.
Deseq2 were used to identified differentially expressed genes. WGCNA analysis were performed to identify gene modules highly correlated to phenotype.
Assembly: hg38
Supplementary files format and content: Common seperated value contained TPM value for each gene in each sample

source_name: ips derived neuroal progenitor cells

growth_protocol: Human iPSCs (Passage 10–40) were maintained on vitronectin-coated plates (Life Technologies) with Essential 8 medium, which was changed daily.

extract_protocol:
Total RNA was extracted using RNeasy micro kit (Qiagen) following manufacturer's protocol.
mRNA library construction were performed by Novogene.

value: ips derived neuroal progenitor cells

value: IVNS1ABP KO


title: KO iPSCs derived NPCs, bio rep2


title: Correctted iPSCs derived NPCs, bio rep3

value: CONTROL


title: KO iPSCs derived NPCs, bio rep1


title: Control, rep14

description: Library name: CT_14


title: Correctted iPSCs derived NPCs, bio rep2


title: Control, rep12

description: Library name: CT_12


title: Control, rep13

description: Library name: CT_13


title: Control, rep15

description: Library name: CT_15


title: adBNST, male, CVMS, rep1


title: adBNST, female, CVMS, rep4


title: Control, rep11

description: Library name: CT_11


title: KPO1-rep2_ATAC


title: adBNST, female, CVMS, rep3


title: KPO1-rep1_ATAC


title: KPY2-rep2_ATAC

value: KP-Y


title: adBNST, female, CVMS, rep5


title: MT iPSCs derived NPCs, bio rep3

value: IVNS1ABP MT


title: adBNST, female, CVMS, rep1


title: Correctted iPSCs derived NPCs, bio rep1


title: Control, rep10

description: Library name: CT_10


title: KO ips cells, bio rep3

source_name: human induced pluripotent stem cells

value: human induced pluripotent stem cells


title: KPY2-rep1_ATAC


title: Control, rep9

description: Library name: CT_9


title: KPY1-rep1_ATAC


title: MT iPSCs derived NPCs, bio rep1


title: adBNST, male, control, rep5

value: control


title: adBNST, male, control, rep4


title: adBNST, female, CVMS, rep2


title: Control, rep7

description: Library name: CT_7


title: Control, rep8

description: Library name: CT_8


title: Control, rep6

description: Library name: CT_6


title: KPP, KI696, R3

first: Igor

last: Mačinković

department: 7Department for Immunity of Inflammation

country: Germany

institute: Medical Faculty Mannheim Heidelberg University

description: Library name: Sample 18

data_processing:
Illumina Dragen v4.2.7
Sequence reads were trimmed for adaptor sequences/low-quality sequences using Trimmomatic, v0.40, parameters ILLUMINACLIP: TruSeq3-SE.fa:2:30:10; HEADCROP:12, followd by Cutadapt v5.1, parameters: -a "polyA=A{20}" -a "QUALITY=G{20}" -m 20 -O 20
GENCODE annotation was used to map reads to the Maus genome GRCh39 (GCA_000001635.9) with STAR v2.7.11b, parameters: --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 10 --alignEndsType EndToEnd
Count reads into exons was determined by using the HTSeq-count v1.99.2
Differential gene expression analysis was done with DESeq2, v1.48.1
Assembly: Mus_musculus.GRCm39.114 (GCA_000001635.9)
Supplementary files format and content: tab-delminted text file includes raw count for each Sample

source_name: KPP

extract_protocol:
Samples were collected from 6-well plate well in 0.5 ml RNAzol® RT (Sigma-Aldrich). RNA was extracted following the RNAzol® RT extraction protocol.
Sequencing libraries were generated from 450 ng RNA using the QuantSeq FWD mRNA-Seq V2 Library Prep Kit with UDI (Lexogen) following the manufacturer’s instructions.

value: KPP

value: primary murine lung tumor cells


title: adBNST, male, control, rep3


title: MT iPSCs derived NPCs, bio rep2


title: KO ips cells, bio rep2


title: Correctted ips cells, rep3


title: Control, rep5

description: Library name: CT_5

value: peripheral blood mononuclear cells


title: KPY1-rep2_ATAC


title: Control, rep4

description: Library name: CT_4


title: KPP, KI696, R1

description: Library name: Sample 16


title: adBNST, male, control, rep1

value: neuro, adBNST


title: Control, rep3

description: Library name: CT_3


title: adBNST, female, control, rep4


title: Correctted ips cells, bio rep1


title: KPP, KI696, R2

description: Library name: Sample 17


title: Control, rep2

description: Library name: CT_2


title: Correctted ips cells, bio rep2


title: KPP, DMSO, R1

description: Library name: Sample 13

value: DMSO


title: MT ips cells, bio rep3


title: KP, KI696, R3

description: Library name: Sample 12

source_name: KP

value: KP


title: adBNST, female, control, rep5


title: MT ips cells, bio rep2


title: KP, KI696, R2

description: Library name: Sample 11


title: adBNST, female, control, rep1


title: KO ips cells, bio rep1


title: KP, KI696, R1

description: Library name: Sample 10


title: adBNST, male, control, rep2


title: KPP, DMSO, R3

description: Library name: Sample 15


title: adBNST, female, control, rep2


title: Control, rep1

description: Library name: CT_1


title: KPP, DMSO, R2

description: Library name: Sample 14


title: adBNST, female, control, rep3


title: leukemia cell lines, rockroi

city: Zürich

first: Giulia

middle: Arianna

last: Moro

address: Winterthurerstrasse 190

department: DMLS

country: Switzerland

institute: University of Zurich

description:
Library name: rockroi cell lines
BD Rhapsody

data_processing:
The mapping, barcode filtering and counting was performed using a custom Snakemake pipeline (https://github.com/imallona/rock_roi_method/) based on STARSolo and featureCounts. Count matrices were analysed in R.
Index the reference genome with STAR.
Subset reads matching the WTA cell barcodes and map those to the transcriptome (genome plus GTF) using STARsolo. Detected cell barcodes (cells) are filtered in at two levels: first, by matching to the user-provided cell barcode whitelist; and second, by applying the EmptyDrops algorithm to discard empty droplets. We report two outputs from this step: the filtered-in cells according to the aforementioned filters; and the unbiased, whole-transcriptome WTA count table
Subset reads matching both the TSO CB structure and the filtered in cell barcodes and map those to the transcriptome. Our reasoning is that the expected TSO transcriptional complexity is undefined and not usable to tell apart cells from empty droplets, so we borrow the filtered-in cells from the EmptyDrops results from the WTA analysis.
Map the raw .fastq files to a transcriptome reference containing fused and non-fused BCR and ABL1, as well as fused BCR and ABL1 cDNA sequences around the breakpoint using bwa aln. Information on the CB and UB extracted from the STARsolo .bam file is then appended to this file to determine from which cell the information derives from. Code is available at https://github.com/imallona/rock_roi_paper/tree/leukemia_patient/08_leukemia_cell_lines/bwa_aln_full_fastq_file
Assembly: Human for alignment with STARsolo: GRCh38.p13.genome.fa and gencode.v38.basic.annotation.gtf. Human for aligment to the transcriptome assembly with bwa aln: gencode.v38.pc_transcripts.fa. Additional sequences: fused BCR and ABL1
Supplementary files format and content: STARsolo output files wta: tab-delimited tsv and sparse matrix mtx files; filtered by EmptyDrops barcodes (matrix.mtx, barcodes.tsv, features.tsv)
Supplementary files format and content: STARsolo output files tso: tab-delimited tsv and sparse matrix mtx files; raw counts (matrix.mtx, barcodes.tsv, features.tsv)
Supplementary files format and content: Results from aligment with bwa aln: tab-delimited file containing read id, bwa aln match, start position of read and CB and UB information extracted from the .bam file obtained with STARsolo (results_bwa_aln.csv.gz)
Supplementary files format and content: FASTA file containing referencre sequences used for aligment with bwa aln (leukemia_bwa_aln_reference.fa.gz)
Supplementary files format and content: comma-separated table containing information on cluster annotation for each cell barcode kept for analysis after doublet removal and QC filtering (annotation.csv)

source_name: Mix of SUP-B15, K562 and Loucy cell lines

growth_protocol: SUP-B15, K562 and Loucy suspension cells were cultured and maintained in RPMI with 10% FBS and 1% PIS in cell culture flasks in an incubator at 37°C and 5% CO2.

extract_protocol:
For the cell line sample,  suspended cells were washed once with PBS and filtered through a 70  µm cell strainer. Cells were resuspended in PBS and counted with a Neubauer chamber. One million cells were resuspended in 1 mL of sample buffer and counted again at the BD Rhapsody Scanner. A ratio of 1:1:1 SUP-B15, K562 and Loucy cells was calculated using the BD Rhapsody Scanner and prepared before loading the sample on the BD Rhapsody Express machine. For the patient sample, frozen bone marrow samples were defrosted, washed twice in PBS and cells were counted with Trypan blue to assess sample quality. If the viability was below 75%, the cells underwent dead cell removal using magnetic bead-based dead cell removal (Dead Cell Removal Kit, Miltenyi Biotec) which was performed following the manufacturer's recommendations. Part of the sample was stained with fluorescent antibodies  for enriching non-leukemic live cells by FACS sorting. Bone marrow sample was stained firstly with the viability dye for 10 minutes on ice, washed once with PBS and stained with the antibody mix for 30 minutes at room temperature in darkness. After staining the cells were washed once in PBS and resuspended in PBS for FACS sorting using the BD FACS Aria III Fusion.
Libraries were generated on a BD Rhapsody Express machine. Libraries for both samples were generated with the following changes to the standard BD Rhapsody workflow: 1) addtion of N1 primer to the RPE PCR; 2) addition of ROIseq primers to the pool of randomeres during RPE extension; 3) separate indexing reaction for the samples in which the N1 primer is added; 4) custom sequencing primer


title: lung TB and HIV coinfected replicate 6

city: Galveston

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

institute: UTMB NGS Core

description: Library name: M740-TB-HIV

data_processing:
STAR 2.7.9a
Assembly: GRCh38 and GRCm39
Supplementary files format and content: gene counts data tab delimited text file

source_name: lung

growth_protocol: NOD-SCID/γcnull female mice (strain 005557) were purchased from The Jackson Laboratory (JAX) following injection of with human CD34+ stem cells via an i.v. (intravenous) route and used at 36 weeks of age.

extract_protocol:
RNA extraction was performed using the Qiagen RNeasy mini kit (Cat. 74104), and the RNase-free DNase set (Cat. 79254). RNA quality was assessed with an Agilent Bioanalyzer, and RIN (RNA Integrity Number) values ranged between 9.8 and 10. PolyA+ RNA was purified from ~100 ng of total RNA.
NEBNext Ultra II RNA library kit (New England Biolabs) was used to prepare the sequencing libraries following the manufacturer’s protocol. Libraries (twenty-four) were quantified by qPCR, pooled, and sequenced using a single-end 75 base run on a Next-Seq 550 High-output flow cell at the UTMB Next Generation Sequencing Core.

treatment_protocol: Mtb strain HN878 (Beijing lineage) was cultured to mid-log phase for delivery of aerosol infection with 100 CFU/mouse as previously described (29). HIV-ADA (NIH AIDS Reagent Program) was propagated in human PBMCs and concentrated by Lenti-virus concentrator (Origene, Cat. TR30025) for animal injections. Virus stock was quantified by GHOST cell infections, measuring the Tissue culture infectious dose (TCID) by GFP quantification via flow cytometry. HIV infections were performed via tail vein injection with 100 µL containing 100,000 TCID/ mouse. For the HIV-mono-infection experiments mice were infected with HIV for 14 days, or non-infected. For the acute Mtb-HIV co-infection, mice were infected by the aerosol route with Mtb, or non-infected. At day 21, non- and Mtb-infected groups were further i.v. infected with HIV-1 (strain ADA). All mice were humanely euthanized at experimental day 30, establishing four experimental groups: non-infected, HIV (9 days), Mtb (30 days), and Mtb-HIV (30 days Mtb infection with HIV co-infection during the last 9 days). Lung, spleen, blood, and liver were collected for further assessment and lung was utilized for RNAseq analysis.

value: lung

value: TB and HIV infection


title: Caki-1_sgVHL_rep2

city: Zhengzhou

first: Kenan

last: Zhang

address: Jianshe Street

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Raw data were preprocessed by using fastp version0.19.6.
Filtered reads were aligned to the genome (GRCh38, hg38) assembly using Bowtie2.
PCR duplicates are removed using the sambamba v0.8.1 with default parameters.
Peaks were called using MACS version2 with the significance cut-off p value <= 0.00001.
bigwig files were generated using deepTools.
Assembly: GRCh38, hg38
Supplementary files format and content: BigWig files.

source_name: Caki-1 cells

growth_protocol: Caki-1 cells were maintained according to the ATCC’s recommendation.

extract_protocol:
In sgCTR and sgVHL Caki-1 cells, nuclei were removed from samples and resuspended in the Tn5 transposase reaction mix. For 30 min, the transposition process was incubated at 37°C. After transposition, equimolar Adapter 1 and Adapter 2 were introduced, and the library was amplified using PCR. Libraries were purified using DNA clean beads after the PCR process, and library quality was evaluated with Qubit.
The library preparations were sequenced on an Illumina NovaSeq 6000 platform after cluster creation, yielding 150 bp paired-end reads.

treatment_protocol: The VHL wild-type Caki-1 cells were used to generate control or VHL knockout cells by CRISPR/Cas9-mediated genome editing (sgCTR and sgVHL Caki-1 cells)

value: Caki-1 cells

value: sgVHL


title: NC_ATSVF

city: Shanghai

first: Qiancheng

last: Xiao

address: Building 25, No. 1188, LIANHANG Road, Pujiang Town, Minhang District, Shanghai

institute: Shanghai OE Biotech Co., Ltd

description:
Library name: Sample2
one sample from murine embryonic hindlimb tissue

data_processing:
Raw sequencing data were processed with Cell Ranger count (v5.0.0) to align reads to the mm10 reference genome and generate raw gene–cell count matrices; samples were aggregated with Cell Ranger aggr.
Count matrices were analyzed in Seurat (v4.1.1). Cells with <500 or >5,000 detected genes, <500 UMIs, or >5% mitochondrial transcripts were removed. Ambient RNA contamination was corrected with SoupX (v1.3.0). Potential doublets were detected with DoubletFinder (v2.0.2).
Gene expression values were log-normalized and 2,000 highly variable genes were selected. PCA was performed and significant PCs were determined using ElbowPlot and JackStraw analyses. Batch effects across biological replicates were corrected using fastMNN prior to graph-based clustering.
Cells were clustered using an SNN modularity optimization approach and visualized by UMAP. Differentially expressed genes between clusters were identified using MAST. Initial cell-type annotation was performed with SingleR (v1.4.1) using the Mouse RNA-seq reference dataset, and refined using canonical markers.
Non-immune cells were excluded where indicated and analyses were recomputed on immune-cell populations. Visualizations were generated using Plotly (v4.9.1). Additional downstream analyses included pseudotime inference with Monocle2 (v2.14.0) and cell–cell communication inference with CellChat (v0.0.2); random seeds were fixed for reproducibility.
Assembly: mm10
Supplementary files format and content: Processed data files include Cell Ranger output matrices (filtered_feature_bc_matrix in .h5 and/or .mtx/.tsv formats), cell-level metadata (QC metrics, sample IDs, cluster and cell-type annotations), dimensionality-reduction coordinates (PCA/UMAP), and marker-gene/differential expression result tables. A README file describes file contents and column definitions.

source_name: epididymal white adipose tissue (eWAT)

extract_protocol:
Adipose tissues were minced into small fragments and enzymatically digested in collagenase type I (1 mg/mL) at 37°C for 30–40 min with gentle agitation. The digested tissue was filtered through a 70-µm cell strainer to remove debris, then centrifuged to separate the stromal vascular fraction (SVF) from mature adipocytes. Red blood cells were lysed using ACK lysis buffer. SVF cells were washed and resuspended in PBS containing 0.04% BSA. Cell viability and concentration were assessed by trypan blue exclusion; samples with viability >85% were used for downstream processing.
Single-cell gene-expression libraries were prepared using the Chromium Single Cell 3′ v1 platform (10x Genomics) following the manufacturer’s protocol. Approximately 10,000–13,000 cells were loaded per channel to minimize doublets. Library quality was assessed on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina NovaSeq 6000 in paired-end mode (PE150).

value: epididymal white adipose tissue (eWAT)

value: Stromal vascular fraction (SVF) cells

value: Wild-type

value: High-fat diet feeding

value: Single batch


title: leukemia patient sample, rockroi

description:
Library name: rockroi patient samples
BD Rhapsody

source_name: Bone marrow aspirate

value: Bone marrow aspirate


title: KO_ATSVF

description:
Library name: Sample1
one sample from murine embryonic hindlimb tissue

value: Camk2d myeloid conditional knockout (Camk2d-CKO)


title: lung TB and HIV coinfected replicate 5

description: Library name: M739-TB-HIV


title: KP, DMSO, R3

description: Library name: Sample 9


title: KP, DMSO, R2

description: Library name: Sample 8


title: Caki-1_sgVHL_rep1


title: MT ips cells, bio rep1

value: human induced pluripotent stem cells

value: IVNS1ABP MT


title: lung TB and HIV coinfected replicate 4

description: Library name: M738-TB-HIV


title: CD45+ cells, tumor 77, GEX

city: Innsbruck

first: Dietmar

last: Rieder

address: Innrain 80

department: Biocenter

institute: Medical University of Innsbruck

description:
Library name: tum-77-GEX
GEX (3‘ RNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Bulk RNA sequencing: nf-core/rnaseq v3.14.0 (using nf-core recommended options for Lexogen QuantSeq 3‘ libraries)
Single cell RNA+V(D)J sequencing: Cellranger pipeline v7.1.0
Assembly: Bulk RNA sequencing: GRCm39 (gencode m31 annotation)
Assembly: Single cell RNA sequencing: GRCm38 gex-mm-10-2020 (10x Genomics)
Supplementary files format and content: Bulk RNA sequencing: Tab-separated file includes raw counts for each sample (tsv)
Supplementary files format and content: Single cell RNA sequencing: GEX: Tab-separated values files for barcodes and features (tsv) and matrix files (mtx); VDJ:  Comma-separated contig annotation files (csv)

source_name: tumor

growth_protocol: Bulk RNA sequencing: CAR-T cells were co-cultured at an effector:target ratio of 5:1 with Panc02-EpCAM tumor cells in CAR RPMI.

extract_protocol:
Bulk RNA sequencing: Total RNA was isolated using the RNeasy Micro kit (Qiagen) according to manufacturer’s instructions.
Single cell RNA+V(D)J sequencing: For scRNAseq, tumors were digested in DMEM+++ supplemented with Liberase TL (Merck, 10mg/mL) and DNAse I (Roche, 20mg/mL) for 30min at 37°C 5% CO2. 0.5M EDTA was added for 5min before meshing tumors through a 20µm cell strainer (Corning). Tumor single cell suspensions were stained using CD45 PE (Biolegend, 1:200) for 20min at 4°C. CD45+ leukocytes were flow sorted. Adequate Cell viability and concentration was verified with trypan blue staining and TC10 automated cell counting (Biorad) complemented with hemocytometer visual inspection.
Bulk RNA sequencing: Libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep +UMI method (Lexogen GmbH, Vienna Biocenter). Quality-validated, barcoded libraries were multiplexed and sequenced using Illumina NovaSeq technology.
Single cell RNA+V(D)J sequencing: Cell suspensions were processed with a Chromium single cell controller (10xGenomics) and Chromium Next GEM Single Cell 5' Kit v2 chemistry, targeting 4000-6000 cells per sample. The resulting total RNA and V(D)J libraries were multiplexed and sequenced with Illumina NovaSeq technology, generating in total approximately 700 M read pairs.

value: tumor

value: CD45+ cells

value: memory

value: Nr2f6 CAR-T treated survivor mice, re-challenged with Panc02-EpCAM negative tumors

tag: library type

value: mRNA


title: Caki-1_sgCTR_rep2

value: sgCTR


title: lung TB and HIV coinfected replicate 2

description: Library name: M735-TB-HIV

value: lung

value: TB and HIV infection


title: lung TB and HIV coinfected replicate 1

description: Library name: M732-TB-HIV


title: KPL, KI696, R2

description: Library name: Sample 5

source_name: KPL

value: KPL

value: primary murine lung tumor cells


title: Caki-1_sgCTR_rep1

value: Caki-1 cells


title: KP, DMSO, R1

description: Library name: Sample 7

value: KP

value: DMSO


title: KPL, KI696, R3

description: Library name: Sample 6


title: CD45+ cells, tumor 77, TCR V(D)J

description:
Library name: tum-77-VDJ
VDJ  (TCR) library: read1 file contains cell barcode and UMI; read2 file contains VDJ sequence

value: VDJ


title: lung TB and HIV coinfected replicate 3

description: Library name: M737-TB-HIV


title: CD45+ cells, tumor 66, GEX

description:
Library name: tum-66-GEX
GEX (3‘ RNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: KPL, DMSO, R3

description: Library name: Sample 3


title: CD45+ cells, tumor 61, GEX

description:
Library name: tum-61-GEX
GEX (3‘ RNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: lung HIV infected replicate 5

description: Library name: M713-HIV

value: HIV infection


title: KPL, KI696, R1

description: Library name: Sample 4


title: lung HIV infected replicate 6

description: Library name: M715-HIV


title: Vector

city: New Haven

first: Chuanpeng

last: Dong

state: CT

address: 850 West Campus Dr

department: Genetics

institute: Yale University School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 with --expect-cells=5000 --nosecondary commands.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Single-cell suspensions from lung tissue were collected. The cells were labeled with an anti-human-CD3-PE/Cy7 antibody and a live/dead dye. FACS-sorted cells were gated on CD3+ live cells. Sorted cells from 5 mice were combined and were washed with PBS, and cell numbers and viabilities were assessed by trypan blue staining. The 10,000 CD3+ T cells isolated from the lung were used for scRNA-seq library prep.
scRNA-seq library prep was  following the protocol from 10x Genomics Chromium Next GEM Single Cell 5’ Reagent Kits V2.

value: Lung

value: T cell

value: Vector


title: 4II

description: 10x Genomics


title: lung HIV infected replicate 4

description: Library name: M709-HIV


title: CD45+ cells, tumor 66, TCR V(D)J

description:
Library name: tum-66-VDJ
VDJ  (TCR) library: read1 file contains cell barcode and UMI; read2 file contains VDJ sequence

value: tumor

value: CD45+ cells


title: A1_OE_2

description: Library name: Sample14

data_processing:
Alignment of sequencing reads was performed using STAR version 2.7.9a .Read count of aligned reads was performed with HTSeq version 0.9.157. Before differential expression analysis, genes with an average read count of less than 3 were excluded. Differential expression analysis was performed with DESeq2 version 1.34.0 58 in R version 4.1.2
Assembly: GRCm39
Supplementary files format and content: counts.txt

extract_protocol:
Total RNAs were extracted with the RNeasy Plus Mini kit
RNA sequencing libraries were prepared according to the Smart-seq2 protocol

value: primary lung tumor

value: KP-O

value: epithelial cells

value: KrasG12D; p53 fl/fl


title: CD45+ cells, tumor 5, GEX

description:
Library name: tum-5-GEX
GEX (3‘ RNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: memory

value: Nr2f6 CAR-T treated survivor mice, re-challenged with Panc02-EpCAM negative tumors

value: mRNA


title: KPL, DMSO, R2

description: Library name: Sample 2

value: KPL

value: primary murine lung tumor cells


title: CD45+ cells, tumor 61, TCR V(D)J

description:
Library name: tum-61-VDJ
VDJ  (TCR) library: read1 file contains cell barcode and UMI; read2 file contains VDJ sequence


title: A1_OE_3

description: Library name: Sample15


title: KPL, DMSO, R1

description: Library name: Sample 1

value: DMSO


title: CD45+ cells, tumor 5, TCR V(D)J

description:
Library name: tum-5-VDJ
VDJ  (TCR) library: read1 file contains cell barcode and UMI; read2 file contains VDJ sequence

value: VDJ


title: A1_OE_4

description: Library name: Sample16


title: A1_OE_1

description: Library name: Sample13


title: lung HIV infected replicate 2

description: Library name: M707-HIV

value: lung

value: HIV infection


title: lung HIV infected replicate 3

description: Library name: M708-HIV


title: CD45+ cells, tumor 43, GEX

description:
Library name: tum-43-GEX
GEX (3‘ RNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: naive

value: naive mice, challenged with Panc02-EpCAM negative tumors


title: tPVAT PRDM16cKO M3

description: Library name: PRDM16cKO_thoracic_PVAT_M3

data_processing:
Transcript expressions were calculated using the Salmon quantification software (version 1.8.1)  and gene expression levels as TPMs and counts retrieved using Tximport (version 1.30.0). Normalization and rlog transformation of raw read counts in genes were performed using DESeq2 (version 1.42.1). For visualisation in genome browsers, RNA-seq reads are aligned to the genome using Rsubread's subjunc method (version 2.8.2) and exported as bigWigs normalised to reads per million using the rtracklayer package (version 1.54.0).  GSEA analysis of gene set enrichment was performed using the fgsea (version 1.28.0)  with the MsigDB pathway gene sets (version v2022.1.Mm).
Assembly: Sequence and transcript coordinates for mouse mm10 genome and ensembl gene models were retrieved from UCSC (GRC Mouse Build 38).
Supplementary files format and content: bulk_rawcounts.csv

source_name: Thoracic aortic perivascular adipose tissue

extract_protocol:
tPVAT and aPVAT were collected, snap frozen in liquid nitrogen and stored at -80˚C. Frozen samples were pulverization in a liquid nitrogen pre-cooled metal cell crusher and total RNA was extracted by TRIzol (Invitrogen). Tissue powder was mixed with TRIZol and incubated under constant rotation for 15min at 4˚C for full lysis and centrifuged to pellet cell debris. Supernatant was used to purified total RNA using chloroform, Ethanol and RNeasy Micro Kit (Qiagen).
At the Rockefeller Genomics Resource Center RNA quality was measured by the Agilent 2100 bioanalyzer chip and samples prepared with Illumina Stranded mRNA Prep, Ligation (96 Samples) /Catalog 20040534 with IDT for Illumina RNA UD Indexes Set B, Ligation (96 Indexes, 96samples).

value: 11 week old

value: Prdm16flox, AdipoQCre+


title: lung HIV infected replicate 1

description: Library name: M706-HIV


title: A1_ctrl_4

description: Library name: Sample12

value: primary lung tumor


title: CD45+ cells, tumor 43, TCR V(D)J

description:
Library name: tum-43-VDJ
VDJ  (TCR) library: read1 file contains cell barcode and UMI; read2 file contains VDJ sequence

value: tumor

value: CD45+ cells


title: tPVAT PRDM16cKO M2

description: Library name: PRDM16cKO_thoracic_PVAT_M2

value: Thoracic aortic perivascular adipose tissue


title: tPVAT PRDM16cKO M1

description: Library name: PRDM16cKO_thoracic_PVAT_M1


title: A1_ctrl_3

description: Library name: Sample11

value: KP-O

value: epithelial cells

value: KrasG12D; p53 fl/fl


title: Y2_OE_4

description: Library name: Sample8

value: KP-Y


title: tPVAT PRDM16cKO M4

description: Library name: PRDM16cKO_thoracic_PVAT_M4


title: A1_ctrl_2

description: Library name: Sample10


title: CD45+ cells, tumor 41, GEX

description:
Library name: tum-41-GEX
GEX (3‘ RNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: mRNA


title: lung TB infected replicate 5

description: Library name: M727-TB

value: TB infection


title: aPVAT PRDM16cKO M1

description: Library name: PRDM16cKO_abdominal_PVAT_M1

source_name: abdominal aortic perivascular adipose tissue


title: CD45+ cells, tumor 41, TCR V(D)J

description:
Library name: tum-41-VDJ
VDJ  (TCR) library: read1 file contains cell barcode and UMI; read2 file contains VDJ sequence

value: VDJ


title: aPVAT PRDM16cKO M4

description: Library name: PRDM16cKO_abdominal_PVAT_M4

value: abdominal aortic perivascular adipose tissue


title: Y2_OE_3

description: Library name: Sample7


title: A1_ctrl_1

description: Library name: Sample9


title: lung TB infected replicate 4

description: Library name: M725-TB

value: lung


title: tPVAT Ctr M4

description: Library name: Control_thoracic_PVAT_M4


title: CD45+ cells, tumor 34, TCR V(D)J

description:
Library name: tum-34-VDJ
VDJ  (TCR) library: read1 file contains cell barcode and UMI; read2 file contains VDJ sequence

value: naive


title: CD45+ cells, tumor 34, GEX

description:
Library name: tum-34-GEX
GEX (3‘ RNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: naive mice, challenged with Panc02-EpCAM negative tumors


title: aPVAT PRDM16cKO M3

description: Library name: PRDM16cKO_abdominal_PVAT_M3

value: 11 week old


title: lung TB infected replicate 1

description: Library name: M721-TB


title: Y2_OE_2

description: Library name: Sample6


title: tPVAT Ctr M3

description: Library name: Control_thoracic_PVAT_M3


title: lung mock infected replicate 6

description: Library name: M720-Mock

value: Mock Infection


title: Y2_OE_1

description: Library name: Sample5

value: primary lung tumor


title: lung TB infected replicate 6

description: Library name: M729-TB


title: Y2_ctrl_4

description: Library name: Sample4


title: CD45+ cells, tumor 33, TCR V(D)J

description:
Library name: tum-33-VDJ
VDJ  (TCR) library: read1 file contains cell barcode and UMI; read2 file contains VDJ sequence

value: tumor


title: lung TB infected replicate 3

description: Library name: M724-TB


title: tPVAT Ctr M2

description: Library name: Control_thoracic_PVAT_M2


title: Knockout, Day8, biol rep 2

description:
Library name: KO_D8_2
3‘ RNA
KO_D8_2

source_name: CAR-T cells

value: CAR-T cells

value: Nr2f6 KO

value: co-culture with Panc02-EpCAM cells

tag: time

value: Day 8


title: CD45+ cells, tumor 33, GEX

description:
Library name: tum-33-GEX
GEX (3‘ RNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: CD45+ cells


title: Knockout, Day8, biol rep 1

description:
Library name: KO_D8_1
3‘ RNA
KO_D8_1


title: Knockout, Day8, biol rep 3

description:
Library name: KO_D8_3
3‘ RNA
KO_D8_3


title: tPVAT Ctr M1

description: Library name: Control_thoracic_PVAT_M1

value: Thoracic aortic perivascular adipose tissue


title: aPVAT Ctr M3

description: Library name: Control_abdominal_PVAT_M3


title: lung mock infected replicate 5

description: Library name: M719-Mock


title: lung mock infected replicate 3

description: Library name: M716-Mock


title: Y2_ctrl_3

description: Library name: Sample3

value: KP-Y

value: epithelial cells

value: KrasG12D; p53 fl/fl


title: lung TB infected replicate 2

description: Library name: M722-TB

value: TB infection


title: aPVAT Ctr M4

description: Library name: Control_abdominal_PVAT_M4

value: abdominal aortic perivascular adipose tissue


title: Wildtype, Day8, biol rep 1

description:
Library name: WT_D8_1
3‘ RNA
WT_D8_1

value: WT

value: mRNA


title: lung mock infected replicate 4

description: Library name: M717-Mock

value: lung


title: pair4, intra, 100% CICI, rep3

city: State College

first: Yi

state: PA

address: 406 SOUTH FREAR, UNIVERSITY PARK

institute: Penn State University

description: Library name: pair4_100_rep3

data_processing:
Next generation sequencing was performed on NextSeq 2000, and 100 million of  50 bp paired-end reads were generated for each replicate. Hi-C data analysis was performed with HiC-pro (version 3.1.0), cooler(version 0.10.0), cooltools (version 0.7.0) and HiCExplorer (version 3.7.2).
Assembly: sacCer3
Supplementary files format and content: cool files

organism: Saccharomyces cerevisiae

source_name: strain

growth_protocol: Yeast strains were grown in 200 mL SCD-Met medium until OD660 reached 0.3.

extract_protocol:
Standard method was used to perform Hi-C and extract DNA.
Hi-C libraries were prepared with NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: To arrest cells in the G1 phase, 80 µM alpha-factor (Zymo, Y1001) was added to the culture for a total of 2.5 hours. During the final hour of this incubation, 1 ng/µL rapamycin was added to induce CICI. DMSO was added in the control group instead. After 1 hour of rapamycin treatment, cells were harvested for imaging analysis and Hi-C measurement.

value: strain

value: MATa, tor1-1, fpr::NAT, bar1, HIS3::REV1pr-tetR-mCherry-REV1pr-LacI-GFP, ADE2::REV1pr-LacI-FKBP12-REV1pr-TetR-FRB, Chr15::433546_LacO, Chr15::966177_TetO, MYO1-CFP-KanMx, NUP49-CFP-KanMx

value: 100% CICI cell + 0% DMSO cell


title: Y2_ctrl_2

description: Library name: Sample2

source_name: primary lung tumor

value: primary lung tumor


title: Y2_ctrl_1

description: Library name: Sample1


title: lung mock infected replicate 2

description: Library name: M705-Mock

value: Mock Infection


title: cellPool.2

description:
CRISPR-seq
APCM_readCounts.tsv.gz
APCM_log2normalized_data.tsv.gz

data_processing:
Raw single-end fastq read files were filtered and demultiplexed using Cutadapt. Raw fastq read files were then trimmed to the 20 bp sgRNA spacer sequences. The 20 bp sgRNA spacer sequences from each demulitplexed sample were mapped the sgRNA spacers to the mSAM library using Bowtie 1.1.2: bowtie -v 2 --suppress 4,5,6,7 --chunkmbs 2000 –best. Using the resultant mapping output, we quantitated the number of reads that had mapped to each sgRNA within the library.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include read counts for each Sample
Library strategy: CRISPR-seq

source_name: E0771-APCM library cells

extract_protocol:
The genomic DNA was extracted Lysis Buffer (50 mM Tris, 50 mM EDTA, 1% SDS, pH 8.0), Proteinase K and RNase A. DNA was precipitated by isopropanol.
The sgRNA library readout was performed using a two-step PCR strategy, where the first PCR includes enough genomic DNA to preserve full library complexity and the second PCR adds appropriate sequencing adapters to the products from the first PCR.

value: E0771-APCM library cells

tag: mouse id


title: Wildtype, Day8, biol rep 3

description:
Library name: WT_D8_3
3‘ RNA
WT_D8_3

value: CAR-T cells

value: co-culture with Panc02-EpCAM cells

value: Day 8


title: aPVAT Ctr M2

description: Library name: Control_abdominal_PVAT_M2

value: 11 week old


title: aPVAT Ctr M1

description: Library name: Control_abdominal_PVAT_M1


title: Wildtype, Day8, biol rep 2

description:
Library name: WT_D8_2
3‘ RNA
WT_D8_2


title: pair4, intra, 0% CICI, rep3

description: Library name: pair4_0_rep3

value: 0% CICI  cell + 100% DMSO cell


title: Knockout, Day4, biol rep 3

description:
Library name: KO_D4_3
3‘ RNA
KO_D4_3

value: Nr2f6 KO

value: Day 4


title: lung mock infected replicate 1

description: Library name: M703-Mock


title: cellPool.1


title: GAT4.4R


title: pair5, inter, 100% CICI, rep2

description: Library name: pair5_100_rep2

value: MATa, tor1-1, fpr::NAT, bar1, HIS3::REV1pr-tetR-mCherry-REV1pr-LacI-GFP, ADE2::REV1pr-LacI-FKBP12-REV1pr-TetR-FRB, Chr15::433546_LacO, Chr4::916282_TetO, MYO1-CFP-KanMx, NUP49-CFP-KanMx


title: Knockout, Day4, biol rep 1

description:
Library name: KO_D4_1
3‘ RNA
KO_D4_1


title: Wildtype, Day4, biol rep 3

description:
Library name: WT_D4_3
3‘ RNA
WT_D4_3

value: WT


title: KO_4

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

description: Library name: Sample 9

data_processing:
Reads were mapped to the mouse reference genome (GRCm38/mm10) and quantified using the CLC Genomics Workbench (version 12.0, QIAGEN). The read counts were normalised by calculating the number of reads per kilobase per million reads (RPKM) for each transcript in individual samples using CLC Genomics Workbench software (version 12.0, QIAGEN).
Assembly: GRCm38/mm10
Supplementary files format and content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

source_name: Embryo

growth_protocol: To generate the Mettl18-/- mice, CRISPR-Cas9 system was used. The 20-mer oligonucleotides (5’-AACGGTGTGCATAGAAAAAG-3’ and 5’-TAGAGCATTTGCTAGCGTGC-3’) located upstream of the PAM site were selected as target sequences for the design of the sgRNA using CRISPRdirect (Naito Y. et al. 2014). The designated sgRNAs were co-expressed with the Cas9 protein using the pX330 vector, then sgRNAs and Cas9 protein were microinjected into fertilized C57BL/6J zygotes.

extract_protocol:
Whole embryos (E18.5) were frozen in liquid nitrogen and were crushed into powder using a Multi-beads Shocker (Yasui Kikai). Then, total RNA was extracted using ISOGEN II (Nippon Gene).
Approximately 500 ng of RNA were ribosomal RNA-depleted using NEBNext rRNA Depletion Kit (New England Biolabs), and converted to Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs). RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Embryo

tag: strain

tag: developmental stage

value: Embryonic day 18.5, Male

value: Mettl18 knockout


title: KO_1

description: Library name: Sample 6


title: GAT4.4L


title: pair5, inter, 50% CICI, rep2

description: Library name: pair5_50_rep2

value: strain

value: 50% CICI cell + 50% DMSO cell


title: Wildtype, Day4, biol rep 2

description:
Library name: WT_D4_2
3‘ RNA
WT_D4_2

value: mRNA


title: Knockout, Day4, biol rep 2

description:
Library name: KO_D4_2
3‘ RNA
KO_D4_2


title: pair5, inter, 10% CICI, rep2

description: Library name: pair5_10_rep2

value: 10% CICI  cell + 90% DMSO cell


title: KO_3

description: Library name: Sample 8


title: KO_5

description: Library name: Sample 10


title: GAT4.3R

value: E0771-APCM library cells


title: pair5, inter, 0% CICI, rep2

description: Library name: pair5_0_rep2


title: KO_2

description: Library name: Sample 7


title: GAT4.3NC


title: pair5, inter, 20% CICI, rep2

description: Library name: pair5_20_rep2

value: 20% CICI cell + 80% DMSO cell


title: Wildtype, Day4, biol rep 1

description:
Library name: WT_D4_1
3‘ RNA
WT_D4_1

value: CAR-T cells

value: co-culture with Panc02-EpCAM cells


title: pair4, intra, 100% CICI, rep2

description: Library name: pair4_100_rep2

value: MATa, tor1-1, fpr::NAT, bar1, HIS3::REV1pr-tetR-mCherry-REV1pr-LacI-GFP, ADE2::REV1pr-LacI-FKBP12-REV1pr-TetR-FRB, Chr15::433546_LacO, Chr15::966177_TetO, MYO1-CFP-KanMx, NUP49-CFP-KanMx

value: 100% CICI cell + 0% DMSO cell


title: GAT4.3LR


title: Knockout, Day0, biol rep 3

description:
Library name: KO_D0_3
3‘ RNA
KO_D0_3

value: Nr2f6 KO

value: Day 0


title: WT_3

description: Library name: Sample 3

value: Wild-type


title: Knockout, Day0, biol rep 2

description:
Library name: KO_D0_2
3‘ RNA
KO_D0_2


title: GAT4.2NC


title: pair4, intra, 20% CICI, rep2

description: Library name: pair4_20_rep2


title: GAT4.3L


title: WT_5

description: Library name: Sample 5


title: WT_4

description: Library name: Sample 4


title: pair4, intra, 50% CICI, rep2

description: Library name: pair4_50_rep2


title: GAT4.2R


title: Wildtype, Day0, biol rep 2

description:
Library name: WT_D0_2
3‘ RNA
WT_D0_2

value: WT


title: Knockout, Day0, biol rep 1

description:
Library name: KO_D0_1
3‘ RNA
KO_D0_1


title: Wildtype, Day0, biol rep 3

description:
Library name: WT_D0_3
3‘ RNA
WT_D0_3


title: WT_1

description: Library name: Sample 1

value: Embryo


title: GAT4.1L


title: WT_2

description: Library name: Sample 2

value: Embryonic day 18.5, Male


title: Wildtype, Day0, biol rep 1

description:
Library name: WT_D0_1
3‘ RNA
WT_D0_1


title: β-cat4A 56hr replicate 5

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

description:
Library name: Mut_m19
B-cat4A Veh

data_processing:
Filtering using Xenome
Alignment using STAR
Quantification using RSEM
Assembly: hg38
Supplementary files format and content: Quantification using RSEM

source_name: Pancreas

growth_protocol: Orthopic tumour model

extract_protocol: Illumina stranded

treatment_protocol: ETC-159 bid

value: Pancreas

value: HPAF-II

value: Cancer

tag: timepoint


title: pair3, intra, 100% CICI, rep2

description: Library name: pair3_100_rep2

value: strain

value: MATa, tor1-1, fpr::NAT, bar1, HIS3::REV1pr-tetR-mCherry-REV1pr-LacI-GFP, ADE2::REV1pr-LacI-FKBP12-REV1pr-TetR-FRB, Chr15::433546_LacO, Chr15::612715_TetO, MYO1-CFP-KanMx, NUP49-CFP-KanMx


title: pair3, intra, 50% CICI, rep2

description: Library name: pair3_50_rep2

value: 50% CICI cell + 50% DMSO cell


title: pair4, intra, 0% CICI, rep2

description: Library name: pair4_0_rep2

value: 0% CICI  cell + 100% DMSO cell


title: GAT4.2L

value: E0771-APCM library cells


title: SCN_L_CT6_4

city: Bethesda

first: Samer

last: Hattar

address: 9000 Rockville Pike

department: National Institute of Mental Health

institute: National Institutes of Health

description:
Library name: S18
10X Genomics

data_processing:
Read alignment, aggregation, barcode processing, and gene expression matrix generation were completed with CellRanger 6.0.0 software (10X Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Anterior hypothalamus

extract_protocol:
Tissues were pooled from three mice per CT. Nuclei extractions were performed by detergent-mechanical cell lysis followed by homogenization and sucrose density gradient as described in Matson et al., 2018.
Libraries were generated with the 3′ single-cell gene expression solution V3 (10X Genomics) according to manufacturer’s instructions.

treatment_protocol: Mice housed under 12L:12D cycles were kept in darkness for one day prior to tissue collection to prevent any effects from prior light exposure. A light pulse was then applied for 15 minutes either at circadian time 6 (CT6), or CT14, or CT22. Hypothalamus tissue containing the SCN was collected 45 minutes after exposure.

value: Anterior hypothalamus

value: L

tag: ct time


title: pair3, intra, 20% CICI, rep2

description: Library name: pair3_20_rep2

tag: cell line

value: 20% CICI cell + 80% DMSO cell


title: GAA21.4R

tag: cell type


title: SCN_D_CT14_3

description:
Library name: S16
10X Genomics

tag: genotype

value: D


title: β-cat4A 56hr replicate 4

description:
Library name: Mut_m18
B-cat4A Veh

tag: treatment


title: GAA21.4NC


title: SCN_D_CT14_4

description:
Library name: S17
10X Genomics


title: pair4, intra, 10% CICI, rep2

description: Library name: pair4_10_rep2

value: MATa, tor1-1, fpr::NAT, bar1, HIS3::REV1pr-tetR-mCherry-REV1pr-LacI-GFP, ADE2::REV1pr-LacI-FKBP12-REV1pr-TetR-FRB, Chr15::433546_LacO, Chr15::966177_TetO, MYO1-CFP-KanMx, NUP49-CFP-KanMx

value: 10% CICI  cell + 90% DMSO cell


title: pair3, intra, 10% CICI, rep2

description: Library name: pair3_10_rep2


title: GAA21.4L


title: GAA21.4LR


title: β-cat4A 56hr replicate 3

description:
Library name: Mut_m16
B-cat4A Veh

tag: batch


title: SCN_D_CT22_3

description:
Library name: S14
10X Genomics

tag: tissue


title: VEC-3_S10

description: Bulk RNA-seq

data_processing:
FASTQ files were aligned to the mouse genome reference version gencode.vM32 by STAR 2.7.10b. Reads mapped to each gene were counted using --quantMode GeneCounts in STAR.
Assembly: gencode.vM32
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: E0771 cells

extract_protocol:
RNA was  extracted by TRIZOL.
The RNA sequencing library was prepared using the NEBNext rRNA Depletion Kit v2 and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina

value: E0771 cells

value: AAV-Vector


title: pair3, intra, 0% CICI, rep2

description: Library name: pair3_0_rep2


title: SCN_L_CT6_3

description:
Library name: S13
10X Genomics


title: β-cat4A 56hr replicate 2

description:
Library name: Mut_m15
B-cat4A Veh


title: pair5, inter, 50% CICI, rep1

description: Library name: pair5_50_rep1

value: MATa, tor1-1, fpr::NAT, bar1, HIS3::REV1pr-tetR-mCherry-REV1pr-LacI-GFP, ADE2::REV1pr-LacI-FKBP12-REV1pr-TetR-FRB, Chr15::433546_LacO, Chr4::916282_TetO, MYO1-CFP-KanMx, NUP49-CFP-KanMx


title: SCN_D_CT14_2

description:
Library name: S11
10X Genomics


title: SCN_D_CT14_1

description:
Library name: S10
10X Genomics


title: VEC-1_S1

description: Bulk RNA-seq


title: pair5, inter, 100% CICI, rep1

description: Library name: pair5_100_rep1

value: 100% CICI cell + 0% DMSO cell


title: pair5, inter, 0% CICI, rep1

description: Library name: pair5_0_rep1


title: INFG-2_S12

description: Bulk RNA-seq

value: AAV-IFNG


title: β-cat4A 16hr replicate 3

description:
Library name: Mut_m12
B-cat4A Veh

value: Pancreas

value: HPAF-II

value: Cancer


title: SCN_D_CT22_2

description:
Library name: S12
10X Genomics


title: pair4, intra, 100% CICI, rep1

description: Library name: pair4_100_rep1

value: strain


title: INFG-3_S6

description: Bulk RNA-seq


title: β-cat4A 16hr replicate 5

description:
Library name: Mut_m4
B-cat4A Veh


title: SCN_D_CT22_4

description:
Library name: S15
10X Genomics


title: pair5, inter, 20% CICI, rep1

description: Library name: pair5_20_rep1


title: pair4, intra, 50% CICI, rep1

description: Library name: pair4_50_rep1

value: 50% CICI cell + 50% DMSO cell


title: pair5, inter, 10% CICI, rep1

description: Library name: pair5_10_rep1


title: SCN_D_CT6_2

description:
Library name: S09
10X Genomics


title: β-cat4A 16hr replicate 4

description:
Library name: Mut_m14
B-cat4A Veh


title: β-cat4A 16hr replicate 2

description:
Library name: Mut_m11
B-cat4A Veh


title: β-cat4A 56hr replicate 1

description:
Library name: Mut_m13
B-cat4A Veh


title: SCN_D_CT6_1

description:
Library name: S08
10X Genomics


title: INFG-1_S11

description: Bulk RNA-seq


title: β-cat4A 4hr replicate 5

description:
Library name: Mut_m9
B-cat4A Veh


title: β-cat4A 16hr replicate 1

description:
Library name: Mut_m10
B-cat4A Veh


title: SCN_D_CT22_1

description:
Library name: S07
10X Genomics


title: VEC-2_S2

description: Bulk RNA-seq


title: SCN_L_CT14_3

description:
Library name: S06
10X Genomics