title: 021355_14-Day_S1_PBS_ROI-005_Secretory

description: Library name: DSP-1001660006709-D-C02

value: PBS


title: 021355_14-Day_S1_OVCAR3_ROI-004_Secretory

status: Public on Jul 15 2025

type: SRA

city: Kansas City

first: Andrew

last: Godwin

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology

country: USA

institute: Kansas University Medical Center

description: Library name: DSP-1001660006709-D-C01

library_source: transcriptomic

data_processing:
FASTQ files downloaded from the NextSeq are converted into the DCC file format using the GeoMxNGSPipeline (version-2.3.3.10).
Initial quality control and data analyses were performed using the GeoMxWorkflows, NanoStringNCTools, and GeoMxTools packages provided on Bioconductor, following the vignette “Analyzing GeoMx-NGS RNA Expression Data with GeoMxTools” provided by NanoString.
Assembly: GRCh38.p13
Supplementary files format and content: .dcc: probe count data
Supplementary files format and content: .pkc: probe metadata linking probe barcodes with target genes IDs
Supplementary files format and content: .xlsx: annotation file containing segment annotation info
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) slides were prepared following the “RNA Slide Preparation Protocol” in MAN-10150 in the Manual Slide Preparation User Manual, available from NanoString. The RNA probe hybridization solution was prepared using the GeoMx® Cancer Transcriptome Atlas (CTA) RNA probe mix (NanoString), following the recommended dilution (10% probe mix + 10% DEPC water + 80% Buffer R).
Library prep was performed according to instructions provided in NanoString’s NGS Readout Library Prep User Manual (MAN-10117-05), followed by paired-end (27 x 27 ) sequencing on the Illumina NextSeq 550 sequencer using a high-output flow cell.

tag: tissue

tag: treatment

tag: patient

tag: roi

tag: days

tag: segment

value: Secretory

tag: nuclei

tag: area


title: miRNA-seq of motor neuron axons treated with vehicle, rep 2

city: ראשון לציון

first: Iddo

last: Magen

state: Not in US

address: בן אליעזר 32, 17

country: Israel

institute: Weizmann Institute

description:
Library name: Sample 8
column name in miRNA_axons_EVs.txt: Axon2

data_processing:
Read alignment using GeneGlobe pipeline (Qiagen) for small RNA, or GenCode for mRNA
low-abudnant sample filtering
DESEq2 for differential expression
Assembly: GRCm38 for small RNA, GRCm39 for mRNA
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Comma-separated values file includes differential expression analysis

molecule: polyA RNA

organism: Mus musculus

source_name: motor neuron

extract_protocol:
RNA extraction MN axonal RNA was extracted from outer compartment of radial MFCs at 14DIV. Axonal RNA was extracted by removing the PBS (from prior wash) from the outer compartment and adding 100µL Qiazol lysis reagent (Qiagen). Inner well was filled with higher volume of PBS to disable the inward flow of lysis reagent towards the inner (soma) compartment and prevent soma contamination. Axons washed off the plate by pipetting the Qiazol around the outer well for 30 seconds. RNA from somata in the inner compartment was extracted with 100µL Qiazol reagent, and lysate was collected in a similar manner. cDNA for axon and soma was prepared with High-Capacity Reverse Transcription Kit (Thermo; Cat. 4368814). Exosomal RNA was extracted by dissolving the exosomal pellet in 700µL Qiazol. RNA was extracted using the RNAeasy micro kit (Qiagen) according to manufacturer’s protocols and RNA yield was quantified using Qubit fluorometer Qubit fluorometer (RNA broad range assay kit; ThermoFisher Scientific). For standard whole-cell RNA preparations from MN / muscle cultures, cultures were lysed in 700µL TRI reagent, and RNA was isolated with ordinary chloroform, isopropanol precipitation protocol.
small RNA libraries were constructed using the QIAseq miRNA library kit following manufacturer's instructions. mRNA libraries were constructed with the MARS-seq protocol (Keren-Shaul et al., Nat. Prot. 2019)

value: motor neuron

tag: cell line

value: motor neuron axons

tag: cell type

tag: genotype

value: WT

value: vehicle

tag: batch


title: miRNA-seq of motor neuron axons treated with vehicle, rep 1

address: בן אליעזר 32, 17

description:
Library name: Sample 7
column name in miRNA_axons_EVs.txt: Axon1


title: 5929-606950_1-Day_S1_PBS_ROI-005_Secretory

description: Library name: DSP-1001660006709-D-D01


title: Sotorasib, 5 days, Rep3

city: La Jolla

first: Eric

middle: S.

last: Wang

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Metabolism and Microenvironment Program

institute: Sanford Burnham Prebys Medical Discovery Institute

description: Library name: D5_Sot_3

data_processing:
Data was processed using nf-core rnaseq pipeline version 3.14.0 (star_rsem) using human genome version GRCh38.p14 and Gencode annotations versions 45.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited table of counts and transcripts-per-million (TPM)

source_name: MIA PaCa-2

extract_protocol:
Total RNA was extracted from cells using the Direct-zol RNA Miniprep Plus kit (Zymo Research #2072)
PolyA RNA isolation and library preparation was performed with the Watchmaker mRNA Library Prep Kit (Watchmaker Genomics: 7BK0001 ) with xGEN Stubby adaptors (IDT, Cat: 336338420) and xGEN 10nt UDIs (IDT, Cat: 336338436). Libraries were sequenced with the Element Biosciences AVITI Sequencing platform using the AVITI 2x75 High Output Cloudbreak Freestyle Kit (Element Biosciences, Cat: 860-00015).

value: MIA PaCa-2

value: PDAC

value: Sotorasib, 5 days


title: miRNA-seq of EVs isolated from primary muscle cultures conditioned medium, rep 3

address: בן אליעזר 32, 17

description:
Library name: Sample 6
column name in miRNA_EV_lysate_muscles.txt: EV_WT3

source_name: muscle

value: muscle

value: primary muscle culture


title: 021355_14-Day_S1_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660006709-D-B10


title: Sotorasib, 5 days, Rep2

description: Library name: D5_Sot_2


title: 021355_14-Day_S1_PBS_ROI-002_Secretory

description: Library name: DSP-1001660006709-D-B11


title: 5929-607140_14-Day_S1_OVCAR3_ROI-008_Secretory

description: Library name: DSP-1001660006709-D-B09


title: induced sputum from COPD patient 5

type: RNA

city: TLALPAN

first: SALVADOR

middle: GARCIA

last: CARMONA

state: CIUDAD DE MÉXICO

address: Calz. de Tlalpan 4502

department: INVESTIGACION

country: Mexico

institute: INSTITUTO NACIONAL DE ENFERMEDADES RESPIRATORIAS

description: Cell-free genomic DNA of induced sputum from COPD patient 5

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina EPIC Infinium Methylation microarray Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: The whole process of the data obtained from the microarray from the intensity data files (IDAT), the quality control of the intensity detection values, the elimination of non-hybridized probes and the results of differentially methylated sites were analyzed using the Rstudio environment version 3.5. 1, using different packages installed in Rstudio, for data normalization and differentially methylated sites analysis the limma package was used implementing a quantile normalization procedure, generating M values and B values used for statistical analysis of methylation data and data visualization. Comparison between the methylation of the 2 groups included in the study was performed by analyzing the m-value matrix in limma obtaining moderated t-statistics and associated p-values for each CpG site by adjusting the p-values for multiple testing, the data obtained in the study were exported from the Rstudio environment as csv files.

label: Cy3 and Cy5

source_name: induced sputum

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was isolated with the Blood DNA Preparation - Solution Kit, Jena Bioscience (Jena, Germany).

value: induced sputum

tag: Sex

value: Famale

value: induced sputum cells

tag: disease state

value: COPD patient 5


title: miRNA-seq of EVs isolated from primary muscle cultures conditioned medium, rep 2

address: בן אליעזר 32, 17

description:
Library name: Sample 5
column name in miRNA_EV_lysate_muscles.txt: EV_WT2


title: 5929-607140_14-Day_S1_PBS_ROI-006_Secretory

description: Library name: DSP-1001660006709-D-B07


title: miRNA-seq of EVs isolated from primary muscle cultures conditioned medium, rep 1

address: בן אליעזר 32, 17

description:
Library name: Sample 4
column name in miRNA_EV_lysate_muscles.txt: EV_WT1


title: DMSO, 5 days, Rep3

description: Library name: D5_DMSO_3

value: DMSO, 5 days


title: 5929-607140_14-Day_S1_OVCAR3_ROI-007_Secretory

description: Library name: DSP-1001660006709-D-B08


title: miRNA-seq of whole cell lysate from primary muscle cultures, rep 3

address: בן אליעזר 32, 17

description:
Library name: Sample 3
column name in miRNA_EV_lysate_muscles.txt: Lys_WT3


title: Sotorasib, 5 days, Rep1

description: Library name: D5_Sot_1


title: DMSO, 5 days, Rep2

description: Library name: D5_DMSO_2


title: 5929-607140_14-Day_S1_PBS_ROI-005_Secretory

description: Library name: DSP-1001660006709-D-B06


title: 5929-607140_14-Day_S1_FT240_ROI-003_Secretory

description: Library name: DSP-1001660006709-D-B04


title: 5929-607140_14-Day_S1_FT240_ROI-002_Secretory

description: Library name: DSP-1001660006709-D-B03


title: 461-27304_1-Day_S2_PBS_ROI-004_Secretory

description: Library name: DSP-1001660005136-B-D05


title: 5929-607140_14-Day_S1_PBS_ROI-004_Secretory

description: Library name: DSP-1001660006709-D-B05


title: 021355_14-Day_S1_FT240_ROI-006_Secretory

description: Library name: DSP-1001660006709-D-C03


title: 5929-607140_14-Day_S1_FT240_ROI-001_Secretory

description: Library name: DSP-1001660006709-D-B02


title: 021355_14-Day_S1_FT240_ROI-003_Secretory

description: Library name: DSP-1001660006709-D-B12


title: 5929-608036_14-Day_S2_PBS_ROI-009_Secretory

description: Library name: DSP-1001660006709-D-B01


title: miRNA-seq of whole cell lysate from primary muscle cultures, rep 1

address: בן אליעזר 32, 17

description:
Library name: Sample 1
column name in miRNA_EV_lysate_muscles.txt: Lys_WT1


title: 5929-608036_14-Day_S2_PBS_ROI-008_Secretory

description: Library name: DSP-1001660006709-D-A12


title: DMSO, 5 days, Rep1

description: Library name: D5_DMSO_1


title: JWJ-01-306+Sotorasib, 5 days, Rep3

description: Library name: D5_Combo_3

value: JWJ-01-306+Sotorasib, 5 days


title: JWJ-01-306+Sotorasib, 5 days, Rep2

description: Library name: D5_Combo_2


title: 5929-608036_14-Day_S2_PBS_ROI-007_Secretory

description: Library name: DSP-1001660006709-D-A11

value: PBS


title: IRR300 scRNAseq

city: Su Zhou

first: Jun

last: Liu

address: No.92, Zhongnan Street, Industrial Park District

country: China

institute: Children’s Hospital of Soochow University

description: 10X genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed with the Cellranger pipeline (version 3.1.0, 10X Genomics) and mapped to the murine reference genome to generate digital gene expression (DGE) matrices. Cells from different batches were merged together, and expressions were normalized to generate a final gene expression matrix.
The raw data from the Spatial Transcriptomics (ST) assay were processed using SpaceRanger (v2.0.1) to generate the ST spots matrix by performing a series of procedures, including alignment, filtering, barcode counting, and UMI counting. Spots with fewer than 200 genes were excluded from further analysis. Normalization across spots was performed with the SCTransform function (0.3.5), and anchors between the spatial transcriptomics spots were identified using the R package “Seurat” (v4.3.0) in R (v4.2.2). Dimension reduction and clustering were performed using PCA. The first ten PCs were used to generate clusters.
Assembly: mm10
Supplementary files format and content: tab-separated text files

source_name: kidney

extract_protocol:
For single-cell suspension preparation, freshly collected mouse kidneys were rinsed twice with RPMI1640 (Gibco), minced into 3-5 mm3 pieces, and subjected to enzymatic digestion using Multi Tissue Dissociation Kits (130-110-204, Miltenyi Biotec) for 30 min under rotation at 250 rpm/min. Afterward, the cell suspension was filtered and centrifuged at 300 g at 4°C. The cell pellet was collected, resuspended in 1 mL RBC lysis buffer (Sigma) to remove RBCs, and then washed twice with RPMI1640. Cell viability was assessed using Trypan Blue (Gibco), and dead cells were removed using magnetic bead separation with a Dead Cell Removal Kit (130-090-101, Miltenyi Biotec) if the cell viability was less than 85%.
At least 20,000 cells per sample were applied to a single-cell master mix with lysis buffer and reverse transcription reagents, following the User Guide of 10X Genomics Chromium Single Cell 3’ Reagent Kits (10X Genomics). The libraries were subjected to high-throughput sequencing on a NovaSeq6000 platform.

value: kidney

value: wild type


title: 5929-608036_14-Day_S2_OVCAR3_ROI-004_Secretory

description: Library name: DSP-1001660006709-D-A08

value: Secretory


title: IRD7 scRNAseq

description: 10X genomics


title: 5929-608036_14-Day_S2_OVCAR3_ROI-006_Secretory

description: Library name: DSP-1001660006709-D-A10


title: JWJ-01-306+Sotorasib, 5 days, Rep1

description: Library name: D5_Combo_1


title: 5929-608036_14-Day_S2_FT240_ROI-003_Secretory

description: Library name: DSP-1001660006709-D-A07


title: 5929-608036_14-Day_S2_FT240_ROI-003_Ciliated

description: Library name: DSP-1001660006709-D-A06

value: Ciliated


title: IRR300 stRNAseq

description: 10X genomics Visum


title: 5929-608036_14-Day_S2_FT240_ROI-002_Secretory

description: Library name: DSP-1001660006709-D-A05


title: JWJ-01-306, 5 days, Rep3

description: Library name: D5_306_3


title: miRNA-seq of whole cell lysate from primary muscle cultures, rep 2

address: בן אליעזר 32, 17

description:
Library name: Sample 2
column name in miRNA_EV_lysate_muscles.txt: Lys_WT2

value: WT

value: vehicle


title: 5929-608036_14-Day_S2_FT240_ROI-002_Ciliated

description: Library name: DSP-1001660006709-D-A04


title: JWJ-01-306, 5 days, Rep2

description: Library name: D5_306_2

value: MIA PaCa-2

value: PDAC


title: mPFC, BTBR+ASIV_D3

city: chongqing

first: jiahui

last: shi

address: 30 Gaotanyan Street

department: Department of Military Cognitive Psychology

institute: Third Military Medical University (Army Medical University)

description: Parallel sample 3

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5。
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: mPFC

growth_protocol: All experimental animals were housed in standard, clean animal facilities with controlled temperatures, a regular light-dark cycle, and ad libitum access to food and water.

extract_protocol:
Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ASIV and the solvent control were injected (i.p.) into C57 or BTBR mice for seven days.

value: mPFC

value: inbred strain

value: treatment(ASIV)+BTBR


title: JWJ-01-306, 5 days, Rep1

description: Library name: D5_306_1


title: IRD7 stRNAseq

description: 10X genomics Visum


title: 5929-608036_14-Day_S2_FT240_ROI-001_Secretory

description: Library name: DSP-1001660006709-D-A03


title: 461-27304_1-Day_S2_FT240_ROI-005_Secretory

description: Library name: DSP-1001660008157-A-H11


title: 5929-608036_14-Day_S2_FT240_ROI-001_Ciliated

description: Library name: DSP-1001660006709-D-A02


title: 461-27304_1-Day_S2_FT240_ROI-005_Ciliated

description: Library name: DSP-1001660008157-A-H10


title: 461-27304_1-Day_S2_FT240_ROI-004_Ciliated

description: Library name: DSP-1001660008157-A-H08


title: Sotorasib, 3 days, Rep2

description: Library name: D3_Sot_2

value: Sotorasib, 3 days


title: mPFC, BTBR+ASIV_D1

description: Parallel sample 1


title: 461-27304_1-Day_S2_FT240_ROI-004_Secretory

description: Library name: DSP-1001660008157-A-H09


title: Sotorasib, 3 days, Rep3

description: Library name: D3_Sot_3


title: mPFC, BTBR+DMSO_C3

description: Parallel sample 3

value: control+BTBR


title: mPFC, BTBR+ASIV_D2

description: Parallel sample 2


title: Sotorasib, 3 days, Rep1

description: Library name: D3_Sot_1


title: 461-27304_1-Day_S2_OVCAR3_ROI-003_Secretory

description: Library name: DSP-1001660008157-A-H07


title: mPFC, BTBR+DMSO_C2

description: Parallel sample 2


title: 461-27304_1-Day_S2_OVCAR3_ROI-003_Ciliated

description: Library name: DSP-1001660008157-A-H06


title: 461-27304_1-Day_S2_OVCAR3_ROI-002_Secretory

description: Library name: DSP-1001660008157-A-H05


title: DMSO, 3 days, Rep3

description: Library name: D3_DMSO_3

value: DMSO, 3 days


title: 5929-608036_14-Day_S2_OVCAR3_ROI-005_Secretory

description: Library name: DSP-1001660006709-D-A09


title: mPFC, BTBR+DMSO_C1

description: Parallel sample 1


title: DMSO, 3 days, Rep2

description: Library name: D3_DMSO_2


title: mPFC, C57+ASIV_B3

description: Parallel sample 3


title: 461-27304_14-Day_S2_OVCAR3_ROI-009_Secretory

description: Library name: DSP-1001660008157-A-H01


title: 461-27304_1-Day_S2_OVCAR3_ROI-001_Ciliated

description: Library name: DSP-1001660008157-A-H02


title: DSP-1001660006709_NTC

description: Library name: DSP-1001660006709-D-A01

source_name: NTC

value: NTC


title: DMSO, 3 days, Rep1

description: Library name: D3_DMSO_1


title: 461-27304_14-Day_S2_OVCAR3_ROI-009_Ciliated

description: Library name: DSP-1001660008157-A-G12


title: 461-27304_14-Day_S2_OVCAR3_ROI-008_Secretory

description: Library name: DSP-1001660008157-A-G11


title: JWJ-01-306+Sotorasib, 3 days, Rep3

description: Library name: D3_Combo_3

value: JWJ-01-306+Sotorasib, 3 days


title: mPFC, C57+ASIV_B1

description: Parallel sample 1


title: 461-27304_14-Day_S2_OVCAR3_ROI-007_Secretory

description: Library name: DSP-1001660008157-A-G09


title: mPFC, C57+DMSO_A3

description: Parallel sample 3


title: JWJ-01-306+Sotorasib, 3 days, Rep2

description: Library name: D3_Combo_2


title: 461-27304_14-Day_S2_PBS_ROI-006_Secretory

description: Library name: DSP-1001660008157-A-G07

value: PBS


title: JWJ-01-306+Sotorasib, 3 days, Rep1

description: Library name: D3_Combo_1


title: JWJ-01-306, 3 days, Rep3

description: Library name: D3_306_3


title: 461-27304_14-Day_S2_PBS_ROI-006_Ciliated

description: Library name: DSP-1001660008157-A-G06


title: mPFC, C57+DMSO_A2

description: Parallel sample 2


title: 461-27304_14-Day_S2_PBS_ROI-005_Secretory

description: Library name: DSP-1001660008157-A-G05


title: mPFC, C57+DMSO_A1

description: Parallel sample 1


title: 461-27304_1-Day_S2_OVCAR3_ROI-002_Ciliated

description: Library name: DSP-1001660008157-A-H04


title: 461-27304_14-Day_S2_PBS_ROI-005_Ciliated

description: Library name: DSP-1001660008157-A-G04


title: JWJ-01-306, 3 days, Rep2

description: Library name: D3_306_2


title: pine1 - replica 3

city: Milano

first: Vittoria

last: Brambilla

state: Milano

address: Via Celoria, 26

department: Agricoltural and environmental sciences

country: Italy

institute: University of MIlan

data_processing:
fastq-mcf for trimming. FastQC for quality check. STAR to align reads to rice Nipponbare genes. htseq-count to count the number of reads aligned for each gene. R-package DESEQ2 to find differentially expressed genes and print-out the number of normalized reads of each gene for each sample.
Assembly: Os-Nipponbare-Reference-IRGSP-1.0 as reference genome. IRGSP-1.0 version of 2020-06-03 for gene annotation, as GTF file. Both downloadable at https://rapdb.dna.affrc.go.jp/download/irgsp1.html
Supplementary files format and content: Excel file with Normalized reads from DESEQ2. Each column is a sample while each row is a gene. Rap-db (https://rapdb.dna.affrc.go.jp/index.html) nomenclature is used for gene loci. Below the list of reads there is the list of differentially expressed genes found using DESEQ2.

organism: Oryza sativa

source_name: stem and SAM tissue

growth_protocol: Nipponbare wt and pine1 knockout plants were sown in soil in a 16 hour long-day growth chamber. Germination occurred around 5 days after sowing. Samples were taken 20 days after germination.

extract_protocol:
tryzol extraction
After the QC procedures of RNA, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. Then, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: No treatment

value: stem and SAM tissue

value: Nipponbare  - pine1 knockout

value: 20 days after germination


title: 461-27304_1-Day_S2_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660008157-A-H03

value: Secretory


title: 461-27304_14-Day_S2_PBS_ROI-004_Secretory

description: Library name: DSP-1001660008157-A-G03


title: mPFC, C57+ASIV_B2

description: Parallel sample 2

value: WT


title: flox,scRNA

city: Shanghai

first: Weijie

last: Vhen

address: 160, Pujian Road

institute: Renji hospital

data_processing:
Basecalls performed using CASAVA version 1.8
STARSolo was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  MT% < 20%;   Cell Gene Number < Median Gene Number * 2;  Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10(Ensembl release 100)
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: brain

extract_protocol:
Brain tissues were placed in DMEM/F12(Gibco), and cut into small fragments and digested them with collagenase (Invitrogen) for at 37℃. After digestion, the obtained cells were filtered through a filter and collect it into a collection tube.
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

value: brain


title: hilpdacko,scRNA


title: pine1 - replica 2


title: Sotorasib, 1 day, Rep3

description: Library name: D1_Sot_3

value: MIA PaCa-2

value: Sotorasib, 1 day


title: 461-27304_14-Day_S2_PBS_ROI-004_Ciliated

description: Library name: DSP-1001660008157-A-G02

value: Ciliated


title: 461-27304_14-Day_S2_FT240_ROI-003_Secretory

description: Library name: DSP-1001660008157-A-G01


title: JWJ-01-306, 3 days, Rep1

description: Library name: D3_306_1

value: PDAC


title: 461-27304_14-Day_S2_OVCAR3_ROI-008_Ciliated

description: Library name: DSP-1001660008157-A-G10


title: pine1 - replica 1


title: 461-27304_14-Day_S2_FT240_ROI-003_Ciliated

description: Library name: DSP-1001660008157-A-F12


title: Sotorasib, 1 day, Rep2

description: Library name: D1_Sot_2


title: Nipponbare wt - replica 3

value: Nipponbare wt


title: 461-27304_14-Day_S2_OVCAR3_ROI-007_Ciliated

description: Library name: DSP-1001660008157-A-G08


title: MP21_20um_RNA

city: Philadelphia

first: Hongxiang

last: Fu

state: PA

address: 3501 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
For RNA sequencing data, we refined read 2 to extract barcode A, barcode B, and the Unique Molecular Identifier (UMI). Using the Spatial Transcriptomics (ST) pipeline version 1.7.2, this processed data was mapped against the appropriate mouse (mm10) genome references. The gene matrix was then read into Seurat v.5.1.0 as a Seurat object. For DNA methylation sequencing data, we first trimmed adaptors and demultiplexed the fastq files. Biscuit was then used to align to the mouse (mm10) genome references, and CG/CH levels were called. MethSCAn was used to identify variable methylation regions. The methylation level and residual matrices were then read into Seurat v.5.1.0 as Seurat objects for downstream analysis.
Assembly: mm10
Supplementary files format and content: File format: rds. Content: Seurat object that contains RNA counts, methylation levels, methylation residuals matrices

source_name: Mouse brain

extract_protocol:
Frozen tissue slides were thawed at 37°C for 2 minutes, fixed with 1% formaldehyde in PBS with RNase inhibitor for 10 minutes, and quenched with glycine for 5 minutes. The tissue was washed with DPBS-RI and DI water, then permeabilized with Triton X-100 and RNase inhibitor for 30 minutes. After washing with DPBS-RI, the tissue was treated with HCl to disrupt protein structure and remove histones, then washed with a buffer containing RNase inhibitor. A transposition mixture was added and incubated at 37°C for 60 minutes twice. The reaction was stopped with EDTA and RNase inhibitor, and the tissue was washed with NEB3.1 buffer and DPBS-RI before proceeding to the in-situ reverse transcription reaction. mRNAs were then captured by the biotinylated RT-primer (poly-dT primer with UMIs and a universal linker sequence, followed by reverse transcription to synthesize the complementary DNA (cDNA). Both genomic fragments and cDNA in the tissue were then ligated to spatial barcodes A and B sequentially. Barcoded gDNA fragments and cDNA were then released after reverse crosslinking. Afterward, the biotin-labeled cDNA was enriched by the streptavidin bead and separated from the gDNA-contained supernatant.
cDNA was followed by template switching, and the cDNA library construction, whereas, gDNA was followed by Enzymatic Methyl-seq conversion, splint ligation, and DNA library construction. In brief, 200 µl of supernatant was collected for methylated gDNA detection and library construction. The supernatant was purified and eluted in 84 µl of nuclease-free water. The Enzymatic Methylation-seq Conversion module was used to convert unmethylated cytosines to uracil. The DNA sample was divided into PCR tubes, and a TET2 reaction mixture was added. After incubation at 37°C, the sample was purified with SPRI beads and eluted. The separated beads containing cDNA were used to generate a cDNA library. Beads were washed, then incubated in a TSO solution with agitation at room temperature and 42°C. PCR was run, and the clear PCR solution was transferred to qPCR tubes with Evagreen dye. After qPCR, the amplified product was purified with SPRI beads and eluted in nuclease-free water. The Nextera XT DNA Library Prep Kit was used for cDNA library preparation.
Spatial-DMT-seq (Spatial DNA Methylation and RNA Transcriptomic Sequencing)

value: Mouse brain


title: MP21_20um_DNAm

library_source: genomic

molecule: genomic DNA


title: 461-27304_14-Day_S2_FT240_ROI-002_Secretory

description: Library name: DSP-1001660008157-A-F11


title: Sotorasib, 1 day, Rep1

description: Library name: D1_Sot_1


title: Nipponbare wt - replica 2


title: ME13_50um_RNA

source_name: Embryo

value: Embryo


title: 461-27304_14-Day_S2_FT240_ROI-002_Ciliated

description: Library name: DSP-1001660008157-A-F10


title: DMSO, 1 day, Rep3

description: Library name: D1_DMSO_3

value: DMSO, 1 day


title: Nipponbare wt - replica 1


title: ME13_50um_DNAm


title: 461-27304_14-Day_S2_FT240_ROI-001_Secretory

description: Library name: DSP-1001660008157-A-F09


title: DMSO, 1 day, Rep2

description: Library name: D1_DMSO_2


title: ME11_50um_RNA


title: DMSO, 1 day, Rep1

description: Library name: D1_DMSO_1


title: 461-27304_14-Day_S2_FT240_ROI-001_Ciliated

description: Library name: DSP-1001660008157-A-F08


title: JWJ-01-306+Sotorasib, 1 day, Rep3

description: Library name: D1_Combo_3

value: JWJ-01-306+Sotorasib, 1 day


title: ME11_50um_DNAm


title: JWJ-01-306+Sotorasib, 1 day, Rep2

description: Library name: D1_Combo_2


title: 461-27304_14-Day_S1_PBS_ROI-009_Ciliated

description: Library name: DSP-1001660008157-A-F06


title: Small RNAs from Control WT

city: Tokyo

first: Kaoru

last: Sato

address: 35-2 Sakae-cho, Itabashi-ku

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

data_processing:
adaptors were trimmed
mapped to dm6 transcriptome by bowtie2 v2.2.4
normalized by RPM
Genome_build: Drosophila melanogaster dm6
Supplementary_files_format_and_content: total RNA: FPKM+1 values for mapped total RNAs to genes and transposons
Supplementary_files_format_and_content: small RNA: FPKM values of mapped small RNAs to piRNA clusters

organism: Drosophila melanogaster

source_name: Drosophila Oregon-R ovary

growth_protocol: Flies were maintained at 25˚C.

extract_protocol: RNA and small RNA libraries were raised by BGI Inc.

treatment_protocol: Overies were dissected in cold-PBS, and then total RNAs were isolated by ISOGEN (Nippon Gene)

value: ovary

value: wildtype

tag: molecule sub type

value: small RNA


title: Small RNAs from egt8

source_name: Drosophila egt8 mutant ovary

value: egt null mutant egt8


title: ATAC_SGK3 PROTAC_Day 2_rep1

city: 上海市

first: Ben

last: Zhou

address: 岳阳路320号

institute: shanghai institude of nutrition and health, CAS

data_processing:
Data precessing was performed in the Galaxy platform (23.2). Adaptors were trimmed by Cutadapt (4.6 + galaxy 1), pair-end reads were aligned to mm10 using Bowtie2 (2.5.0 + galaxy 0), improperly paired reads and reads with mapQuality < 30 or mapping to the mitochondria were filtered by filter BAM (2.5.2 + galaxy 1). After filtering, reads were subjected to MACS2 (2.2.9.1+ galaxy 0) for peak calling with a FDR q-value ≤0.0000001, visualization was performed by bamCoverage (3.5.4 + galaxy 0). For ATAC-seq, duplicated reads were removed by MarkDuplicates (3.1.1.0) before MACS2 callpeek. For BRG1 CUT&TAG, spike-in counts were generated by Bowtie2 (2.5.0 + galaxy 0) with aligned to spike-in.fastq and used for data correction.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: pre-adipocyte

extract_protocol:
For BRG1 CUT&TAG assays, 100,000 pre-adipocytes were harvest by trysin digestion and counted, CUT&TAG assays were conducted following the manufacturer's instructions (TD903, Vazyme). For ATAC-seq assays, 50,000 pre-adipocytes were harvest by trysin digestion and counted, and then nucleus were extracted, ATAC-seq assays were conducted following the manufacturer's instructions (N248, Novoprotein).
BRG1 CUT&TAG libraries and ATAC-seq libraries were constructed  with extracted DNA fragments mentioned above following the manufacturer's instructions (TD202, Vazyme for BRG1 CUT&TAG or N239, novoprotein for ATAC-seq) respectively. For ATAC-seq libraries, additional fragment selection was conducted with 0.4×/0.8× beads ratio after DNA extraction.

treatment_protocol: For pre-adipocyte differentiation, cells were seeded in growth medium (DMEM supplemented with 10% FBS) 5 days prior to adipogenesis induction. At day 0 (D0), when cells reached confluence, adipogenesis was initiated by treating them with a cocktail containing 5 mg/mL insulin, 0.5 mM 3-isobutyl-1-methyl-xanthine (IBMX), 1 mM dexamethasone, and 1 mM rosiglitazone. For SGK3 PROTAC treatment, cells were exposed to either 0.3 μM SGK3 PROTAC or an equivalent volume of DMSO vehicle two days before harvesting.

value: pre-adipocyte

value: wild type

value: SGK3 PROTAC, MDI


title: Small RNAs from egt17

source_name: Drosophila egt17 mutant ovary

value: egt null mutant egt17


title: Total RNA from egt8

value: Total RNA


title: Small RNAs from Control WT rep2


title: 461-27304_14-Day_S1_PBS_ROI-008_Secretory

description: Library name: DSP-1001660008157-A-F05

value: PBS

value: Secretory


title: 461-27304_14-Day_S1_PBS_ROI-008_Ciliated

description: Library name: DSP-1001660008157-A-F04

value: Ciliated


title: JWJ-01-306, 1 day, Rep3

description: Library name: D1_306_3

value: MIA PaCa-2

value: PDAC


title: Total RNA from egt17


title: ATAC_SGK3 PROTAC_Day -3_rep1

value: SGK3 PROTAC, vehicle


title: JWJ-01-306, 1 day, Rep2

description: Library name: D1_306_2


title: 461-27304_14-Day_S1_PBS_ROI-007_Secretory

description: Library name: DSP-1001660008157-A-F03


title: ATAC_SGK3 PROTAC_Day -3_rep2


title: ATAC_vehicel_Day 2_rep2

value: vehicle, MDI


title: 461-27304_14-Day_S1_PBS_ROI-007_Ciliated

description: Library name: DSP-1001660008157-A-F02


title: JWJ-01-306, 1 day, Rep1

description: Library name: D1_306_1


title: Total RNA from Control WT


title: ATAC_vehicel_Day 2_rep1


title: Total RNA from Control WT rep2


title: 461-27304_14-Day_S1_FT240_ROI-006_Secretory

description: Library name: DSP-1001660008157-A-F01


title: Sotorasib, 5 hr, Rep3

description: Library name: 5h_Sot_3

value: Sotorasib, 5 hr


title: Experiment_2_antibiotics5

city: 1066 Epalinges

first: Jessica

last: Rebeaud

address: Chemin des Boveresses 155

country: Switzerland

institute: University of Lausanne

data_processing:
Data processing was performed by the Lausanne Genomic Technologies Facility (GTF) as follows:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011). Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1).
Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013). Reads were aligned against Mus musculus.GRCm38.98 genome using STAR (v. 2.5.3a, Dobin et al. 2013)
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Mus musculus.GRCm38.92 gene annotation
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012).
Assembly: GRCm38.98
Supplementary files format and content: Tab-delimited text file containing in the first column Ensembl Gene ID, and raw count values in columns 2 for each sample

source_name: Colon

growth_protocol: CD4+ T cells from TCRMOG 2D2+ mice (8-12 weeks old) were isolated and differentiated into pathogenic Th17 cells over 5 days. After restimulation, these cells were injected into wild-type mice to induce EAE. Four days post-transfer, colonic lamina propria lymphocytes were isolated for RNASeq analysis. All experiments were conducted in an SPF facility at Lausanne University, adhering to local animal welfare guidelines.

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit (Qiagen). RNAseq libraries were prepared from 3ng ng of total RNA.
Takara SMART-Seq v4 Ultra Low Input (cDNA synthesis) and Illumina DNA Prep (library prep from the cDNA) was used following manufacturer's protocol.

treatment_protocol: All mice receiving EAE by adotpive transfer (transfer of pathogenic Th17 cells); half of the mice were treated with an antibiotic cocktail (2 weeks enroflaxin, 2 weeks co-amoxicilin)

value: Colon

value: T cell

value: WT

value: Antibiotics


title: 461-27304_14-Day_S1_PBS_ROI-009_Secretory

description: Library name: DSP-1001660008157-A-F07


title: ATAC_vehicel_Day -3_rep2

value: pre-adipocyte

value: vehicle, vehicle


title: Sotorasib, 5 hr, Rep2

description: Library name: 5h_Sot_2


title: JWJ-01-306+Sotorasib, 1 day, Rep1

description: Library name: D1_Combo_1

value: JWJ-01-306+Sotorasib, 1 day


title: 461-27304_14-Day_S1_FT240_ROI-006_Ciliated

description: Library name: DSP-1001660008157-A-E12


title: Sotorasib, 5 hr, Rep1

description: Library name: 5h_Sot_1


title: Experiment_2_antibiotics4


title: ATAC_SGK3 PROTAC_Day 2_rep2

value: wild type

value: SGK3 PROTAC, MDI


title: Experiment_2_antibiotics3


title: DMSO, 5 hr, Rep3

description: Library name: 5h_DMSO_3

value: DMSO, 5 hr


title: 461-27304_14-Day_S1_FT240_ROI-005_Ciliated

description: Library name: DSP-1001660008157-A-E10


title: ATAC_vehicel_Day -3_rep1


title: 461-27304_14-Day_S1_FT240_ROI-005_Secretory

description: Library name: DSP-1001660008157-A-E11

value: Secretory


title: 461-27304_14-Day_S1_FT240_ROI-004_Secretory

description: Library name: DSP-1001660008157-A-E09


title: BRG1_CUT&TAG_SGK3 PROTAC_Day -3_rep2

data_processing:
Data precessing was performed in the Galaxy platform (23.2). Adaptors were trimmed by Cutadapt (4.6 + galaxy 1), pair-end reads were aligned to mm10 using Bowtie2 (2.5.0 + galaxy 0), improperly paired reads and reads with mapQuality < 30 or mapping to the mitochondria were filtered by filter BAM (2.5.2 + galaxy 1). After filtering, reads were subjected to MACS2 (2.2.9.1+ galaxy 0) for peak calling with a FDR q-value ≤0.0000001, visualization was performed by bamCoverage (3.5.4 + galaxy 0). For ATAC-seq, duplicated reads were removed by MarkDuplicates (3.1.1.0) before MACS2 callpeek. For BRG1 CUT&TAG, spike-in counts were generated by Bowtie2 (2.5.0 + galaxy 0) with aligned to spike-in.fastq and used for data correction.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&TAG


title: 461-27304_14-Day_S1_FT240_ROI-004_Ciliated

description: Library name: DSP-1001660008157-A-E08

value: Ciliated


title: DMSO, 5 hr, Rep1

description: Library name: 5h_DMSO_1

value: MIA PaCa-2


title: Experiment_1_antibiotics1


title: Experiment_2_antibiotics1


title: JWJ-01-306+Sotorasib, 5 hr, Rep3

description: Library name: 5h_Combo_3

value: PDAC

value: JWJ-01-306+Sotorasib, 5 hr


title: 461-27304_14-Day_S1_OVCAR3_ROI-003_Secretory

description: Library name: DSP-1001660008157-A-E07


title: BRG1_CUT&TAG_vehicel_Day 2_rep2

value: vehicle, MDI


title: BRG1_CUT&TAG_SGK3 PROTAC_Day -3_rep1

value: SGK3 PROTAC, vehicle


title: 461-27304_14-Day_S1_OVCAR3_ROI-003_Ciliated

description: Library name: DSP-1001660008157-A-E06


title: JWJ-01-306+Sotorasib, 5 hr, Rep2

description: Library name: 5h_Combo_2


title: Experiment_2_control3

value: Colon

value: Untreated


title: 461-27304_14-Day_S1_OVCAR3_ROI-002_Secretory

description: Library name: DSP-1001660008157-A-E05


title: BRG1_CUT&TAG_vehicel_Day 2_rep1


title: JWJ-01-306+Sotorasib, 5 hr, Rep1

description: Library name: 5h_Combo_1


title: Experiment_2_control1

value: T cell

value: WT


title: Experiment_2_control2


title: BRG1_CUT&TAG_SGK3 PROTAC_Day 2_rep2

value: pre-adipocyte


title: BRG1_CUT&TAG_vehicel_Day -3_rep2

value: vehicle, vehicle


title: BRG1_CUT&TAG_SGK3 PROTAC_Day 2_rep1


title: JWJ-01-306, 5 hr, Rep3

description: Library name: 5h_306_3


title: BRG1_CUT&TAG_vehicel_Day -3_rep1


title: Experiment_1_control1


title: JWJ-01-306, 5 hr, Rep2

description: Library name: 5h_306_2


title: DMSO, 5 hr, Rep2

description: Library name: 5h_DMSO_2


title: cKO-scRNA

city: Seoul

first: MinYeong

last: Lim

address: 103, Daehak-ro, Jongno-gu

department: Department of biomedical scicence

country: South Korea

institute: Seoul National University, College of Medicine

library_source: genomic single cell

data_processing:
For scRNA-seq, alignment was performed using the Cell Ranger toolkit (version 6.0.1). For each cell, a filtered gene-cell matrix was obtained by applying two two quality measures:mitochondrial gene percentage (<10%) and the number of detected genes (>200 & <5000) using Seurat v5.0.0.The doublets were detected and removed by using DoubletFinder v2.0.3.The remaining data was normalized and transformed by SCTrasnform with v2 regularization for downstream analysis.
For scATAC-seq, alignment was performed using the Cell Ranger toolkit (version 6.0.1). Two quality measures were used to filter low-quality cells: nFrags > 1000, and TSSenrichment>10. The doublets were detected and removed by using filterDoublets function (filterRatio=1.0) from ArchR v1.0.2. The remaining data was normalized and then used in downstream analysis using ArchR pipeline.
Assembly: mm10
Supplementary files format and content: scATAC fragments files, scRNA filtererd features barcode and normalized count files

source_name: Lung

extract_protocol:
For ATAC-seq, nuclei suspensions were prepared using the FL™ Automated Fluorescence Cell Counter (Logos Biosystems) and incubated in a transposition mix, following the 10x Chromium Multiome ATAC+ Gene Expression protocol (CG000338).  For scRNA-seq, single-cell suspensions were diluted to ~10,000 cells and processed using the Next GEM 3' v3.1 protocol (CG000315).
For scATAC seq transposed nuclei were mixed with master mix, loaded into a Chromium chip, and processed in the Chromium Controller. Post-transposition, samples were amplified, indexed with P7 and sample indices, and qualified using the Agilent 4200 TapeStation. scATAC seq libraries were sequenced on an Illumina HiSeq platform. Single cell ATAC data was analyzed by Cell Ranger ARC v2.0.0 (10x Genomics) was used to generate FASTQ files from raw data. For scRNA-seq, single-cell suspensions were diluted to ~10,000 cells and processed using the Next GEM 3' v3.1 protocol (CG000315). Cells were loaded into a Chromium Next GEM Chip G, barcoded, reverse transcribed, and the resulting cDNA was enriched via PCR. Final cDNA libraries were quantified and qualified using qPCR (KAPA) and Agilent 4200 TapeStation before sequencing on the Illumina HiSeq platform. Single cell gene expression data was analyzed using Cell Ranger v7.0.1 (10x Genomics). Briefly, raw BCL files from Illumina HiSeqXten were demultiplexed to generate FASTQ from raw data. For scRNA seq, extracted  cells were loaded into a Chromium Next GEM Chip G, barcoded, reverse transcribed, and the resulting cDNA was enriched via PCR. Final cDNA libraries were quantified and qualified using qPCR (KAPA) and Agilent 4200 TapeStation before sequencing on the Illumina HiSeq platform. Single cell gene expression data was analyzed using Cell Ranger v7.0.1 (10x Genomics). Briefly, raw BCL files from Illumina HiSeqXten were demultiplexed to generate FASTQ from raw data.

treatment_protocol: Murine lung ILC2 from rmIL-33 treated tamoxifen-inducible Piezo11fl/fl and Piezo11fl/fl Id2-CreERT2 mice were sorted and generating for single cell ATAC and RNA-seq libraries were generated using 10x Genomics platforms.

value: Lung

value: ILCs

value: Piezo1 fl/fl x Id2-Cre ERT2


title: 461-27304_14-Day_S1_OVCAR3_ROI-002_Ciliated

description: Library name: DSP-1001660008157-A-E04


title: 461-27304_14-Day_S1_OVCAR3_ROI-001_Ciliated

description: Library name: DSP-1001660008157-A-E02


title: JWJ-01-306, 5 hr, Rep1

description: Library name: 5h_306_1


title: WT-scRNA

value: Piezo1 fl/fl


title: HAR123-KO, frontal cortex, Rep3

first: Kun

last: Tan

address: 9500 Gilman Drive # 0695

department: Dept. of Obstetrics, Gynecology & Reproductive Science

institute: UCSD

data_processing:
Reads were filtered for quality and aligned with STAR (2.5.2b) against the GRCm38 (Ensembl version 96).
The exon counts were aggregated for each gene to build a read count table using SubRead function featureCounts.
Differentially expressed genes (DEGs) were defined using DESeq2 using the following threshold: |Log2FC| > 1, and q-val < 0.01. The R package program pheatmap was used for clustering and generating heatmap plots.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited txt file including raw counts for each sample

source_name: frontal cortex from 8-weeks old mice

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen), following the manufacturer’s protocol. Ribosomal RNAs were removed using NEBNext® rRNA Depletion Kit v2 (New England Biolabs).
Purified RNAs were used to make the library using the NEBNext Ultra II Directional RNA Library Prep kit (New England Biolabs), as per manufacturer's instructions. Libraries were sequenced (pair-end reads) with an Illumina NovaSeq 6000 platform for 100 cycles at the UCSD institute for Genomic Medicine (IGM) core.

value: frontal cortex from 8-weeks old mice


title: 461-27304_1-Day_S1_FT240_ROI-004_Secretory

description: Library name: DSP-1001660008157-A-E01

value: Secretory


title: sgNS DOX, 5 days, Rep3

description: Library name: D5_sgNS_dox_3

data_processing:
Data was processed using nf-core rnaseq pipeline version 3.17.0 (star_rsem) using human genome version GRCh38.p14 and Gencode annotations versions 47.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited table of counts and transcripts-per-million (TPM)

source_name: MIA PaCa-2

value: MIA PaCa-2

value: sgNS DOX, 5 days


title: cKO-scATAC


title: HAR123-KO, frontal cortex, Rep2


title: 461-27304_1-Day_S1_PBS_ROI-003_Secretory

description: Library name: DSP-1001660008157-A-D12

value: PBS


title: sgNS DOX, 5 days, Rep2

description: Library name: D5_sgNS_dox_2

value: PDAC


title: WT-scATAC


title: HAR123-KO, frontal cortex, Rep1


title: 461-27304_1-Day_S1_PBS_ROI-003_Ciliated

description: Library name: DSP-1001660008157-A-D11

value: Ciliated


title: H358,Control,72hour

city: Nagoya

first: Hiromichi

last: Ebi

state: Aichi

address: 1-1, Kanokoden, Chikusa-ku

department: Division of Molecular Therapeutics

institute: Aichi Cancer Center Research Institute

data_processing:
Mapping and peak call were conducted by ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline). Reads were mapped to the GRCh38 reference sequence using Bowtie2 (ver. 2.3.4.3), and duplicate reads were removed with Picard (ver. 2.20.7) and samtools (ver. 1.9).
Assembly: GRCh38
Supplementary files format and content: bigWig

extract_protocol:
The cells (3 E+5) were then trypsinized and cryopreserved in cell stock solution (Bambanker, Nippon Genetics) until processing. ATAC-seq was performed by DNAFORM Life Science Research Center 402 (Yokohama, Japan).
Approximately 300,000 cells were lysed and transposition reaction was performed with the Tn5 Transposase (Illumina Catalog #FC121-1030) at 37°C for 30 minutes. The reaction liquid was purified with Qiagen MinElute PCR Purification Kit. Then 5 cycles of PCR with custom Nextera PCR primers (from Wu and Buenrostro 2013) were conducted using NEBNext Q5 Hot Start HiFi PCR Master Mix (New England Biolabs). Additional number of PCR cycles was determined by qPCR of the partly amplified products, following Wu and Buenrostro 2013. The PCR products were purified with Agencourt AMPure XP beads (Beckman Coulter: A63881), using double size selection (left ratio: 1.4x, right ratio: 0.5x) according to the manufacturer’s protocol.

treatment_protocol: NCI-H358 cells were treated with DMSO or 1uM sotorasib for 72 hour.


title: sgNS DMSO, 5 days, Rep3

description: Library name: D5_sgNS_dmso_3

value: sgNS DMSO, 5 days


title: 461-27304_14-Day_S1_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660008157-A-E03

data_processing:
FASTQ files downloaded from the NextSeq are converted into the DCC file format using the GeoMxNGSPipeline (version-2.3.3.10).
Initial quality control and data analyses were performed using the GeoMxWorkflows, NanoStringNCTools, and GeoMxTools packages provided on Bioconductor, following the vignette “Analyzing GeoMx-NGS RNA Expression Data with GeoMxTools” provided by NanoString.
Assembly: GRCh38.p13
Supplementary files format and content: .dcc: probe count data
Supplementary files format and content: .pkc: probe metadata linking probe barcodes with target genes IDs
Supplementary files format and content: .xlsx: annotation file containing segment annotation info
Library strategy: Spatial Transcriptomics


title: WT, frontal cortex, Rep3


title: HAR123-KO, frontal cortex, Rep4


title: 461-27304_1-Day_S1_PBS_ROI-002_Secretory

description: Library name: DSP-1001660008157-A-D10


title: 461-27304_1-Day_S1_PBS_ROI-002_Ciliated

description: Library name: DSP-1001660008157-A-D09


title: H358,AMG510,72hour


title: WT, frontal cortex, Rep2


title: sgNS DMSO, 5 days, Rep1

description: Library name: D5_sgNS_dmso_1


title: kalta4xuas, 6 dpf, rep10

city: Worcester

first: Summer

last: Thyme

state: MA

address: 364 Plantation St

institute: UMass Chan Medical School

description:
Library name: Sample 10
WT_5_E4_S52

data_processing:
Single-end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner (2.7.3a-GCC-6.4.0-2.28).
The raw counts files from STAR, in this record, were normalized using the rlog method in DESeq2 for subsequent published analysis.
Assembly: GRCz11
Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.
Supplementary files format and content: The identifiers (in the processed data *ReadsPerGene.out.input.tab.gz files) are from the following transcriptome annotation (PMID 32831172):
Supplementary files format and content: https://www.umassmed.edu/lawson-lab/reagents/zebrafish-transcriptome/
Supplementary files format and content: as also listed in the LLgeneID_entrezID.csv, llgeneid_genename.csv

organism: Danio rerio

source_name: head with eyes, 3-5 heads combined

extract_protocol:
RNA was extracted using the MicroElute Total RNA Kit (Omega Bio-Tek R6834-02), with a 15-min incubation with Dnase I.
Libraries were constructed using an in-house protocol based on SMART-Seq2, followed by Nextera XT Library Preparation (FC-131-1096).

value: head with eyes, 3-5 heads combined

value: Tg(4xUAS:hmgn6) siblings


title: kalta4xuas, 6 dpf, rep9

description:
Library name: Sample 9
WT_4_E3_S51


title: 461-27304_1-Day_S1_PBS_ROI-001_Secretory

description: Library name: DSP-1001660008157-A-D08


title: 461-27304_1-Day_S1_PBS_ROI-001_Ciliated

description: Library name: DSP-1001660008157-A-D07


title: WT, frontal cortex, Rep1

value: WT


title: sgZBTB11 #2 DOX, 5 days, Rep3

description: Library name: D5_sg6_dox_3

value: sgZBTB11 #2 DOX, 5 days


title: kalta4xuas, 6 dpf, rep8

description:
Library name: Sample 8
WT_3_E2_S50


title: Adult, snRNAseq

city: Xiamen

first: Lingjuan

last: Zhang

address: Xiangan South Street

institute: Xiamen University

description: 10x Genomics

data_processing:
The raw sequencing data was demultiplexed and aligned to the reference genome mm10-1.2.0 using Cell Ranger v3.0.2 pipiline(10x Genomics).
The generated raw gene expression matrix was converted into Seurat objects using the R package Seurat v2.0.
To remove doublets and poor-quality cells, we utilized the following procedures to control for cell quality: >200 genes/cell, <5000 genes/cell; >25,000 unique molecular identifiers(UMIs)； and <8% mitochondrial gene expression.
Low quality cells and outliers were discarded, and only ～6,943 viable cells were used for downstream analysis.
Unsupervised clustering and gene expression were visualized with the Seurat 2.0 on R studio, and assignment of cell clusters was based on expression of validated marker genes.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: nuclear RNA

source_name: skin

extract_protocol:
Preparation of nuclear suspensions from frozen dermal tissue samples required 200mg or "soybean" sized tissue samples. After tissue collection, non-adherent tissue was removed, residual blood and other fluids were properly drained, and the tissue was cut into 1-2mm3 pieces on ice in a centrifuge. The fragments were transferred to cryotubes and flash-frozen in liquid nitrogen for 5 minutes, after which they could be transferred to an ultra-low temperature refrigerator or stored in liquid nitrogen. The entire sampling and minification process should be completed quickly to avoid RNA degradation.
Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v 2. cDNA libraries were sequenced on an Illumina Novaseq6000 platform (Illumina).

value: skin

tag: age

value: 2 months old

value: mTmG


title: DSP-1001660008157_NTC

first: Andrew

last: Godwin

institute: Kansas University Medical Center

description: Library name: DSP-1001660008157-A-A01

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) slides were prepared following the “RNA Slide Preparation Protocol” in MAN-10150 in the Manual Slide Preparation User Manual, available from NanoString. The RNA probe hybridization solution was prepared using the GeoMx® Cancer Transcriptome Atlas (CTA) RNA probe mix (NanoString), following the recommended dilution (10% probe mix + 10% DEPC water + 80% Buffer R).
Library prep was performed according to instructions provided in NanoString’s NGS Readout Library Prep User Manual (MAN-10117-05), followed by paired-end (27 x 27 ) sequencing on the Illumina NextSeq 550 sequencer using a high-output flow cell.

value: NTC


title: kalta4xuas, 6 dpf, rep7

description:
Library name: Sample 7
WT_2_E1_S49


title: sgZBTB11 #2 DOX, 5 days, Rep2

description: Library name: D5_sg6_dox_2


title: sgNS DOX, 5 days, Rep1

description: Library name: D5_sgNS_dox_1


title: WT, frontal cortex, Rep4


title: sgZBTB11 #2 DOX, 5 days, Rep1

description: Library name: D5_sg6_dox_1


title: scRNA-seq of human soft tissue sarcoma sample - BO112-017-baseline

city: Boston

first: Stefano

last: Testa

state: Massachusetts

address: 330 Brookline Avenue

institute: Beth Israel Deaconess Medical Center

data_processing:
Sample demultiplexing, read alignment, and generation of feature-barcode matrices were performed using CellRanger v6.0.0 (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: Raw feature barcode matrix for downstream analysis

source_name: undifferentiated pleomorphic sarcoma

extract_protocol:
The samples were dissociated using collagenase D (100mg/mL) and DNase I (100mg/mL) using a 100 m cell strainer. Then, after digestion, RBC lysis was performed by adding 1mL of BD lysing buffer (BD Biosciences) and incubating for 5 mins. Cells were counted using a Countess II cell counter (Thermo Scientific).
Libraries were constructed using the Chromium 3’ Gene Expression Solution v3.1 (10x Genomics) per the manufacturer’s instructions.

value: undifferentiated pleomorphic sarcoma

value: tissue

value: tumor


title: scRNA-seq of human soft tissue sarcoma sample - BO112-016-surgery

source_name: liposarcoma

value: liposarcoma


title: sgZBTB11 #2 DMSO, 5 days, Rep3

first: Eric

last: Wang

institute: Sanford Burnham Prebys Medical Discovery Institute

description: Library name: D5_sg6_dmso_3

extract_protocol:
Total RNA was extracted from cells using the Direct-zol RNA Miniprep Plus kit (Zymo Research #2072)
PolyA RNA isolation and library preparation was performed with the Watchmaker mRNA Library Prep Kit (Watchmaker Genomics: 7BK0001 ) with xGEN Stubby adaptors (IDT, Cat: 336338420) and xGEN 10nt UDIs (IDT, Cat: 336338436). Libraries were sequenced with the Element Biosciences AVITI Sequencing platform using the AVITI 2x75 High Output Cloudbreak Freestyle Kit (Element Biosciences, Cat: 860-00015).

value: MIA PaCa-2

value: sgZBTB11 #2 DMSO, 5 days


title: ectomycorrhizal root tips 14d-2

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

country: France

institute: INRAE

description:
Library name: M14Pop_38
This sample is from ectomycorrhizal root tips  at 14d . It is the second of three biological replicates used in this experiment.

data_processing:
Illumina software was used by the Genotoul sequencing facilities (Toulouse, France) to generate fastq raw data files
Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and aligned to the Populus trichocarpa v4.1 primary transcripts available at Phytozome (https://phytozome-next.jgi.doe.gov/info/Ptrichocarpa_v4_1l) using CLC Genomics Workbench v24.. For read mapping the CLC genomic workbench parameters were the following: minimum length fraction 0.9, minimum similarity frac-tion 0.9, Mismatch cost = 2, insertion cost = 3, Deletion cost = 3 and the maximum number of hits for a read was set to 10. The unique mapped reads number for each transcript were determined and then normalized to RPKM (Reads Per Kilobase of exon model per Million mapped reads) and TPM.
We calculated differential expression of genes with DESeq2
Assembly: reference genome sequence of Populus trichocarpa v4.1 (at Phytozome (https://phytozome-next.jgi.doe.gov/info/Ptrichocarpa_v4_1l)
Supplementary files format and content: tab-delimited text file including Phytozome v4.1 ID,  normalised expression values  RPKM and TPM, as well as unique mapped reads

organism:
Laccaria bicolor
Populus tremula x Populus alba

source_name: ectomycorrhizal root tips

growth_protocol: Laccaria bicolor S238N and Populus tremula x alba 717-1B4 in vitro co-cultures were made according to the sandwich system , with small modifications. In brief, L. bicolor was pre-cultured in dark at 25°C for one week on sugar-reduced Pachlewski agar medium P20. P. tremula x alba micro-cuttings were stimulated to root for 1 week on solid Murashige and Skoog  (MS) medium supplemented with 2 mg/L IBA (Indol-3-butyric acid) and subsequently transferred to cellophane covered MS plates. After three weeks of incubation at 25°C with a 16h photoperiod, poplar explants were  transferred to cellophane covered P20 medium supplemented with 0.1% MES. To allow plant-fungal interaction,  the cellophane covered with L. bicolor pre-cultures was placed in an inverted position on the roots.  Control plates, containing control plants  were prepared and handled the  same way as co-cultures. All plates were incubated at 20°C with a 16h photoperiod. Samples (100 mg fresh weight) for RNA extraction were taken after  14  days of (co-)culture from control roots and EcM (i.e. all fungal and mixed plant-fungal material within 0.5 cm distance of a root), snap frozen in liquid nitrogen and stored at -80°C.

extract_protocol:
Total RNA was extracted from control root and mixed plant-fungal biomass (100 mg) using the RNeasy Plant Mini Kit (Qiagen). Biomass was ground in liquid nitrogen prior to extraction and an on column DNAse I treatment was included in the protocol. For samples containing poplar roots (EcM), extraction buffer RLC was supplemented with 2% PEG (polyethylene glycol) 8000.
Preparation of libraries from total RNA (TruSeq Stranded mRNA Kit Illumina) and 2 x 150 bp Illumina HiSeq3000 sequencing was performed at the GET platform (Gé-nopole Toulouse Midi-Pyrénées, Auzeville, France) following their standard protocol.

value: ectomycorrhizal root tips

tag: time

value: 14 days

value: TimecourseJR


title: sgNS DMSO, 5 days, Rep2

address: 10901 North Torrey Pines Road

description: Library name: D5_sgNS_dmso_2

value: PDAC

value: sgNS DMSO, 5 days


title: kalta4xuas, 6 dpf, rep5

description:
Library name: Sample 5
KALTA4_5_D11_S47

tag: tissue

value: head with eyes, 3-5 heads combined

value: Tg(elavl3:KalTA4; 4xUAS:hmgn6)


title: sgZBTB11 #2 DMSO, 5 days, Rep2

description: Library name: D5_sg6_dmso_2

tag: treatment


title: ectomycorrhizal root tips 14d-1

description:
Library name: M14Pop_37
This sample is from ectomycorrhizal root tips at 14d . It is the first of three biological replicates used in this experiment.


title: kalta4xuas, 6 dpf, rep4

description:
Library name: Sample 4
KALTA4_4_D10_S46


title: sgZBTB11 #2 DMSO, 5 days, Rep1

description: Library name: D5_sg6_dmso_1


title: Lung metastasis from mouse treated with cabo + anti-PD-1 for 2 weeks, then switched to lenvatinib.

city: Sapporo

first: KO

last: OKABE

state: Hokkaido

address: South-1, West-16, Chuo-ku

institute: Sapporo Medical University School of Medicine

description:
Library name: ComLenALu
JN00019952data2.xlsx

data_processing:
Reads were quality checked using FastQC v0.11.7
Adapter sequences and low-quality bases were trimmed using Trimmomatic v0.38.
Gene expression levels were quantified using StringTie v2.1.3b to calculate TPM.
Differential expression analysis was performed using edgeR in R/Bioconductor:contentReference
Assembly: mm10
Supplementary files format and content: Tab-delimited text file containing TPM expression values for each gene in each sample. Columns represent sample IDs matching library names; rows represent gene IDs

source_name: lung

growth_protocol: RENCA cells (murine renal adenocarcinoma cell line, CRL-2947, ATCC) were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 100 IU/mL penicillin, and 100 μg/mL streptomycin. Cultures were maintained at 37°C in a humidified incubator with 5% CO2.RENCA cells were orthotopically implanted into the left kidney of BALB/c mice. Tumors were allowed to grow until treatment initiation.

extract_protocol:
Total RNA was extracted from tumor tissues and submitted to Macrogen Inc. (Seoul, Republic of Korea) for library preparation and RNA sequencing:contentReference
Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) following the manufacturer’s instructions:contentReference

treatment_protocol: Mice were treated as follows: (1) untreated control group received no therapy; (2) cabozantinib group received 30 mg/kg orally once daily, 3 days per week; (3) anti-PD-1 antibody group received 200 μg/mouse intraperitoneally once daily, 2 days per week; (4) combination group received both cabozantinib (30 mg/kg orally, 3 days per week) and anti-PD-1 antibody (200 μg/mouse intraperitoneally, 2 days per week); (5) after two weeks of combination therapy, second-line treatment groups received either axitinib (25 mg/kg orally, 3 times per week), everolimus (10 mg/kg orally, 3 times per week), or lenvatinib (10 mg/kg orally, 3 times per week) from the third week onward.

value: lung


title: scRNA-seq of human soft tissue sarcoma sample - BO112-013-baseline


title: Lung metastasis from mouse treated with cabo + anti-PD-1 for 2 weeks, then switched to everolimus

description:
Library name: ComEveBLu
JN00019952data2.xlsx


title: kalta4xuas, 6 dpf, rep3

description:
Library name: Sample 3
KALTA4_3_D9_S45


title: scRNA-seq of human soft tissue sarcoma sample - BO112-015-baseline


title: scRNA-seq of human soft tissue sarcoma sample - BO112-011-baseline


title: sgZBTB11 #1 DOX, 5 days, Rep3

city: La Jolla

description: Library name: D5_sg5_dox_3

value: sgZBTB11 #1 DOX, 5 days


title: Experiment_2_antibiotics2

value: Colon

value: T cell

value: WT

value: Antibiotics


title: kalta4xuas, 6 dpf, rep2

description:
Library name: Sample 2
KALTA4_2_D8_S44


title: Lung metastasis from mouse treated with cabo + anti-PD-1 for 2 weeks, then switched to axitinib.

description:
Library name: ComAxi-1Lu
JN00020801data2.xlsx


title: scRNA-seq of human soft tissue sarcoma sample - BO112-010-baseline

value: undifferentiated pleomorphic sarcoma

value: tissue

value: tumor


title: ectomycorrhizal root tips 14d-3

description:
Library name: M14Pop_39
This sample is from ectomycorrhizal root tips  at 14d . It is the third of three biological replicates used in this experiment.


title: kalta4xuas, 6 dpf, rep1

description:
Library name: Sample 1
KALTA4_1_D7_S43


title: sgZBTB11 #1 DOX, 5 days, Rep2

description: Library name: D5_sg5_dox_2

value: MIA PaCa-2


title: Kidney tumor from a mouse treated with a combination of cabozantinib and anti-PD-1 antibody

description:
Library name: Lt4ComKD
JN00019390data2.xlsx

source_name: kidney

value: kidney


title: kalta4xuas, 6 dpf, rep6

description:
Library name: Sample 6
WT_1_D12_S48

value: Tg(4xUAS:hmgn6) siblings


title: scRNA-seq of human soft tissue sarcoma sample - BO112-009-surgery

value: liposarcoma


title: sgZBTB11 #1 DOX, 5 days, Rep1

description: Library name: D5_sg5_dox_1

value: PDAC


title: Endothelium, Hpa2 loss-of-function, biol rep 2_2

city: Bar Harbor

first: Yannic

last: Becker

state: Maine

address: 159 Old Bar Harbor Road

institute: Mount Desert Island Biological Laboratory

data_processing:
Remove reads with adapter contamination.
Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%).
Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Assembly: GRCz11 zebrafish reference genome
Supplementary files format and content: .xlsx format, gene counts

source_name: Endothelium

growth_protocol: Tg(fli1:EGFP)y1 zebrafish were raised and staged as described. Embryos/larvae were maintained in egg water (0.5x E2 medium) at 28.5°C.

extract_protocol:
60-80 Tg(fli1a:eGFP)y1 Hpa2-loss of function or control larvae were anesthetized and euthanized by icing at 96 hpf. Larvae were washed once with PBS and subsequently dissociated into single cells using a 0.25% (w/v) trypsin 0.53 mmol/l EDTA solution at 30°C, applying gentle mechanical stress by pipetting. The reaction was stopped by adding twice the volume of 10% (v/v) calf serum/DMEM medium followed by two washing steps with PBS (cell pelleting 500x g for 5 min). For FACS sorting, cells were resuspended in sorting buffer (5mmol/l EDTA, 1% (v/v) goat serum in HBSS) and filtered through a 40-µm nylon mesh. Propidium iodide (1 µg/ml) was added directly prior to sorting of GFP+ cells. Sorted cells were kept on ice and RNA was isolated with the use of the RNeasy Plus Micro Kit (Qiagen).
Library construction and sequencing were conducted by Novogene with the ultra low input pipeline for mRNA sequencing

treatment_protocol: Hpa2 loss-of-function was induced by morpholino antisense strategy. Embryos were injected at the one-cell stage with morpholino targeting hpse2 exon‑intron junction 10. A standard control MO (GeneTools) was injected in equimolar amounts.

value: Endothelium

value: wt


title: Lung metastasis from a mouse treated with a combination of cabozantinib and anti-PD-1 antibody

description:
Library name: Lt4Com
JN00017379data2.xlsx


title: Endothelium, Hpa2 loss-of-function, biol rep 2_1


title: sgZBTB11 #1 DMSO, 5 days, Rep2

description: Library name: D5_sg5_dmso_2

value: sgZBTB11 #1 DMSO, 5 days


title: sgZBTB11 #1 DMSO, 5 days, Rep1

description: Library name: D5_sg5_dmso_1


title: Kidney tumor from a mouse treated with anti-PD-1 antibody

description:
Library name: Rt3Lt1NivoKD
JN00019390data2.xlsx


title: Endothelium, Hpa2 loss-of-function, biol rep 1_2


title: Lung metastasis from a mouse treated with anti-PD-1 antibody

description:
Library name: Rt3Lt1Nivo
JN00017379data2.xlsx

value: lung


title: scRNA-seq of human soft tissue sarcoma sample - BO112-007-baseline


title: scRNA-seq of human soft tissue sarcoma sample - BO112-004-baseline

source_name: myxofibrosarcoma

value: myxofibrosarcoma


title: sgNS DOX, 3 days, Rep2

description: Library name: D3_sgNS_dox_2

value: sgNS DOX, 3 days


title: sgNS DOX, 3 days, Rep3

description: Library name: D3_sgNS_dox_3


title: Kidney tumor from a mouse treated with cabozantinib

description:
Library name: Rt3caboKD
JN00019390data2.xlsx


title: Endothelium, control, biol rep 2_2

value: control


title: sgNS DOX, 3 days, Rep1

description: Library name: D3_sgNS_dox_1


title: Lung metastasis from a mouse treated with cabozantinib

description:
Library name: Rt3cabo
JN00017379data2.xlsx


title: S461585_WTA_Scan 2_014

city: Birmingham

first: Claudio

last: Mauro

address: University of Birmingham

department: Institute of Immunology and Immunology

country: United Kingdom

institute: University of Birmingham

data_processing:
FASTQ files were processed using the GeoMX NGS pipeline (2.0.0.16) to produce dcc files
dcc files were uploaded to the GeoMx DSP for downstream analysis
Data were filtered using default settings and normalised using Q3 normilisation
Assembly: N/A
Supplementary files format and content: dcc files containing raw counts
Library strategy: Spatial Transcriptomics

source_name: coronary artery

extract_protocol:
5μm thick FFPE slides were cut using a microtome. Deparaffin Protocol - Xylene 5min x3, 100% EtOH 5min x2, 95% EtOH 5min x1. 99°C ER2 (Ph9) 15mins. 37°C 1μg/mL Proteinase K 15mins. 10%NBF 5min, NBF Stop buffer 5min x2. 37°C. Label Protocol - WTA probe mix 1:10 16hr. 37°C 50%Formamide-2xSSC mix 25mins x2. Hybridisation Protocol - Syto13, CD45  TxRed, CD4 647 60mins. Scan Protocol - FITC - SYTO1350ms, TxRed - CD45 200ms, Cy5 - CD4 200ms
Spatial transcriptome sequencing libraries were prepped with Nanostring Reagent kits according to manufacturer's suggestions.

value: coronary artery

tag: subset

tag: grade

tag: localisation

value: Negative control


title: Kidney tumor from a mouse that was observed without any treatment

description:
Library name: NewLt2HolesKD
JN00019390data2.xlsx


title: Endothelium, control, biol rep 2_1


title: S461585_WTA_Scan 2_013

tag: roi


title: sgNS DMSO, 3 days, Rep3

description: Library name: D3_sgNS_dmso_3

value: sgNS DMSO, 3 days


title: S461585_WTA_Scan 2_011

value: Mild

value: Adventitia


title: Endothelium, control, biol rep 1_1


title: sgNS DMSO, 3 days, Rep2

description: Library name: D3_sgNS_dmso_2

value: MIA PaCa-2


title: Tumor under no treatment; Tumor under Kras-inhibitor treatment

description:
Library name: SL-D1
FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using Space Ranger v3.0.1 (10x Genomics) to align reads to the mouse genome (mm10).
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5: An HDF5 file containing the gene expression matrix, barcode list, and feature list (genes).
Supplementary files format and content: scalefactors_json.json: scalefactors in json format.
Supplementary files format and content: tissue_positions.csv: lit of spatial barcodes.
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Library strategy: Spatial Transcriptomics

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) tissue samples were sectioned at a thickness of 5 µm using a microtome and mounted onto Visium HD Spatial Gene Expression slides (10x Genomics, Inc., Pleasanton, CA, USA). Tissue sections were subjected to hematoxylin and eosin (H&E) staining following the manufacturer’s protocol. Images were acquired at 20× magnification using a high-resolution bright-field microscope (VS-200, Evident Corp., Tokyo, Japan) and used for subsequent spatial alignment.
Hybridization of mRNA from the tissue sections to barcoded oligonucleotide probes on the slide surface was performed using CytAssist (10x Genomics), followed by library preparation, including cDNA synthesis and amplification, fragmentation, and adapter ligation, according to the manufacturer’s instructions.

value: Lung

value: LLC

value: no-treatment; Kras-inhibitor


title: sgNS DMSO, 3 days, Rep1

description: Library name: D3_sgNS_dmso_1

value: PDAC


title: S461585_WTA_Scan 2_010


title: Lung metastasis from a mouse that was observed without any treatment

description:
Library name: NewLt2holes
JN00017379data2.xlsx


title: scRNA-seq of human soft tissue sarcoma sample - BO112-009-baseline

value: liposarcoma

value: tissue

value: tumor


title: Endothelium, Hpa2 loss-of-function, biol rep 1_1

value: Endothelium

value: wt


title: T_A3

city: Hengyang

first: Rui

last: Chen

address: No. 336 Dongfeng Road

institute: Nanhua Hospital Affiliated to University of South China

description: Library name: Sample 12

data_processing:
This 16S analysis pipeline conducts quality control on raw sequencing data by first using fastp to filter and trim low-quality reads, then employing cutadapt in QIIME2 to remove primers, and finally applying DADA2's denoise-paired function in QIIME2 to denoise sequences, remove chimeras, and generate ASV tables and representative sequences.
Assembly: silva-138-99
Supplementary files format and content: tab-delimited text files include all samples' absolute quantitative value for each identified taxonomy
Library strategy: 16S rRNA-seq

organism: Rattus norvegicus

source_name: feces

extract_protocol:
DNA was isolated by grinding, shaking, centrifugation, adsorption, elution with Mixed lysis buffer (buffer) containing Proteinase K, Isopropyl alcohol buffer solution, Ethanol buffer solution, ddH2O and so on.
Microbial DNA was extracted from fecal samples, and the 16S rRNA gene region was amplified using specific primers. The amplified DNA fragments were used to construct sequencing libraries. High-throughput sequencing, typically performed using the Illumina platform, was conducted to generate sequence data.

value: feces

value: adipogenuc differentiation


title: T_A2

description: Library name: Sample 11


title: sgZBTB11 #2 DOX, 3 days, Rep2

description: Library name: D3_sg6_dox_2

value: sgZBTB11 #2 DOX, 3 days


title: sgZBTB11 #2 DOX, 3 days, Rep1

description: Library name: D3_sg6_dox_1


title: S461585_WTA_Scan 2_012

value: coronary artery

value: Negative control


title: T_A1

description: Library name: Sample 10


title: S461585_WTA_Scan 2_009

value: Mild


title: S_T3

description: Library name: Sample 9


title: Tumor under anti-Cd47ab treatment;  Tumor under a combination therapy of anti-Cd47ab and Kras-inhibitor

description:
Library name: SL-A1
FFPE Spatial transcriptome sequencing

value: anti-Cd47ab; Combination of anti-Cd47ab and Kras-inhibitor


title: Endothelium, control, biol rep 1_2

value: control


title: sgZBTB11 #2 DMSO, 3 days, Rep3

description: Library name: D3_sg6_dmso_3

value: MIA PaCa-2

value: sgZBTB11 #2 DMSO, 3 days


title: S461585_WTA_Scan 2_007

value: Normal

value: Adventitia


title: S461585_WTA_Scan 2_006


title: sgZBTB11 #2 DOX, 3 days, Rep3

description: Library name: D3_sg6_dox_3

value: PDAC


title: S461585_WTA_Scan 2_008


title: S461585_WTA_Scan 2_005


title: S_T2

description: Library name: Sample 8


title: E12.5_cut_3hpa_3

city: Montpellier

first: Jholy

last: De la cruz

state: hérault

address: 80 avenue Augustin Fliche

institute: INSERM U1183

description: Gene expression data from E12.5 embryos post-amputation flank tissues

hyb_protocol: A hybridization cocktail is prepared, including the fragmented target, probe array controls, BSA, and herring sperm DNA. It is then hybridized to the probe array during a 16-hour incubation. Immediately following hybridization, the probe array undergoes an automated washing and staining protocol.

scan_protocol: Data was acquired on a GeneChip® Scanner 3000 and CEL file generation performed using AGCC. Affymetrix Expression Console™ following standard Exon Array protocols.

data_processing: Robust Multi-chip Average (RMA) was used to extract probe intensity data

label: biotin

label_protocol: cDNA synthesis, amplifcation, fragmentation and biotinylation were performed using the Ambion WT Expression Kit (Ambion, Austin, TX, USA)

growth_protocol: Rolling bottle culture system was used to maitain embryos alive and perform regeneration experimetn

extract_protocol: Dissection of amputation flanking tissues was performed followed by Total RNA extraction using the Rneasy Mini Kit from Qiagen

treatment_protocol: Microsurgery

value: post-amputation flank tissue

tag: Stage

tag: time point


title: sgZBTB11 #2 DMSO, 3 days, Rep2

description: Library name: D3_sg6_dmso_2

tag: cell line


title: S461585_WTA_Scan 2_004


title: sgZBTB11 #2 DMSO, 3 days, Rep1

description: Library name: D3_sg6_dmso_1

tag: cell type


title: S_T1

description: Library name: Sample 7


title: S461585_WTA_Scan 2_003


title: SAH3

description: Library name: Sample 6


title: sgZBTB11 #1 DOX, 3 days, Rep3

description: Library name: D3_sg5_dox_3

value: sgZBTB11 #1 DOX, 3 days


title: E12.5_cut_1hpa_3


title: E12.5_cut_3hpa_1


title: E12.5_cut_1hpa_2


title: SAH2

description: Library name: Sample 5


title: E12.5_cut_3hpa_2


title: S461585_WTA_Scan 2_002


title: sgZBTB11 #1 DOX, 3 days, Rep2

description: Library name: D3_sg5_dox_2


title: SAH1

description: Library name: Sample 4


title: Sham3

description: Library name: Sample 3


title: S461585_WTA_Scan 2_001


title: S461588_WTA_017


title: E12.5_cut_0hpa_3


title: sgZBTB11 #1 DMSO, 3 days, Rep3

description: Library name: D3_sg5_dmso_3

value: sgZBTB11 #1 DMSO, 3 days


title: Sham2

description: Library name: Sample 2


title: sgZBTB11 #1 DMSO, 3 days, Rep2

description: Library name: D3_sg5_dmso_2


title: S461588_WTA_016


title: E12.5_cut_0hpa_2


title: sgNS DOX, 1 day, Rep3

description: Library name: D1_sgNS_dox_3

value: sgNS DOX, 1 day


title: E10.5_cut_3hpa_3

description: Gene expression data from E10.5 embryos post-amputation flank tissues


title: E10.5_cut_3hpa_2


title: NSCs, H4

city: Changsha

first: Chaoyong

last: He

address: Tianma road

institute: Hunan university

data_processing:
Reads mapping and gene expression quantification: cDNA library samples were sequenced as described above. After removing the reads with adapters, any reads containing ‘n’ (> 10%) and low-quality reads (sQ ≤ 5), the remaining clean reads were checked by FastQC (v.0.11.5). Clean reads were aligned to the Rattus norvegicus Rnor 6.0.98 using STAR (v.2.5.3a) and the raw counts matrix were obtained by featureCounts. The expression level of genes was calculated using CPM (count per millon) as a metric, and filtered using the sum of relative abundance to eliminate the effects of sequencing depths.
PCA analysis, DEG obtain and clustering: Normalized gene expression values used to calculate the correlation coefficient among biological replicates for PCA and hierarchical clustering. The PCA was calculated with the prcomp function in R with default settings. Hierarchical clustering was performed using the pheatmap package with default settings using Pearson’s correlation. The DEGs in pairwise comparisons were identified by the R package edgeR, which performs data normalization using the trimmed mean of M-values (TMM) method. Genes with at least a two-fold change in expression and P value < 0.05 were considered to be expressed differentially. A k-means approach was used (R package pheatmap) to cluster all the DEGs identified through pairwise comparisons.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: brain tissue from SD rats at 1 day

growth_protocol: NSCs were isolated from cerebral cortices of 1–day-old neonatal Sprague-Dawley rats.

extract_protocol:
NSCs were expanded as neutrospheres at 37°C, 5% CO2 for 3-4 days in proliferation culture medium, which contained DMEM/F12 supplemented with 1% glutamine (Gibco), 1% sodium pyruvate (Gibco), 1% NEAA (Gibco), 2% B27 (Gibco), 0.02 ng/mL EGF, 0.02 ng/mL bFGF, 1.83 ng/mL heparin and 1% streptomycin penicillin (Gibco). The proliferation medium was replaced every 2 days. Thereafter, the NSCs neutrospheres were gathered through centrifugation (300×g, 5min), and digested with 0.25% trypsin-EDTA (Gibco) at 37℃ for 18 min. After terminating digestion mixture using 10% FBS, the cells were collected by countrification and filtered through 70 μm and 40 μm mech of cell strainer successively to obtain the NSCs of single-cell suspension. 0.2% (W/V) of Col solution mixed with equal volume of NSCs single-cell suspension to obtain final 0.75, 1.5, 3 million/mL of cell packing density system.
RNA-seq library preparation. Total RNA was isolated from each sample using the RNAmini kit (Qiagen, Germany). RNA quality was examined by gel electrophoresis and with Qubit (Thermo, Waltham, MA, USA). Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA), through reverse transcription using S1000TM Touch Thermal Cycler (Bio Rad) at 53°C (45 min) - 85°C (5 min) - 4°C cycle. The generated cDNA was amplified, and quality estimated using Agilent 4200 (performed by CapitalBio Technology, Beijing). The sequences of libraries were finally obtained using the Illumina Novaseq6000 sequencer with pair-end 150 bp (PE150).

treatment_protocol: After tissue pieces of dissociation, the mixed cortical cells were first passed through a 100 μm mesh of nylon cell strainer, then plated into tissue culture flasks.

tag: strain

value: Sprague-Dawley

value: brain tissue

value: Neural Stem Cells

tag: genotype

value: wild type

value: 1 day-old

value: High cell packing density


title: S461588_WTA_014

value: coronary artery

value: Muscle


title: sgNS DOX, 1 day, Rep2

description: Library name: D1_sgNS_dox_2

value: MIA PaCa-2


title: S461588_WTA_015

value: Moderate


title: E12.5_cut_1hpa_1


title: NSCs, H2


title: sgZBTB11 #1 DOX, 3 days, Rep1

description: Library name: D3_sg5_dox_1


title: E12.5_cut_0hpa_1


title: S461588_WTA_018


title: E10.5_cut_3hpa_1


title: Sham1

description: Library name: Sample 1

value: feces

value: adipogenuc differentiation

tag: batch


title: sgNS DOX, 1 day, Rep1

description: Library name: D1_sgNS_dox_1

value: PDAC


title: S461588_WTA_013

value: Plaque


title: NSCs, H1


title: S461588_WTA_012

value: Infiltrated muscle layer


title: E10.5_cut_1hpa_3

value: post-amputation flank tissue


title: sgZBTB11 #1 DMSO, 3 days, Rep1

description: Library name: D3_sg5_dmso_1

value: sgZBTB11 #1 DMSO, 3 days


title: NSCs, M4

value: Sprague-Dawley

value: Medium cell packing density


title: sgNS DMSO, 1 day, Rep2

description: Library name: D1_sgNS_dmso_3

value: sgNS DMSO, 1 day


title: S461588_WTA_011


title: sgNS DMSO, 1 day, Rep1

description: Library name: D1_sgNS_dmso_2


title: E10.5_cut_1hpa_1


title: E10.5_cut_0hpa_3


title: S461588_WTA_010

value: Mild

value: Adventitia


title: sgZBTB11 #2 DOX, 1 day, Rep2

description: Library name: D1_sg6_dox_2

value: sgZBTB11 #2 DOX, 1 day


title: S461588_WTA_009

value: coronary artery


title: E10.5_cut_0hpa_2


title: NSCs, M2

value: brain tissue

value: Neural Stem Cells

value: wild type

value: 1 day-old


title: NSCs, M1


title: Healthy donor 3 P6529 CD8SP

city: Madrid

first: María

middle: L

last: Toribio

state: Madrid

address: Calle Nicolás Cabrera, 1. Campus Cantoblanco

department: Interactions with the environment

country: Spain

institute: Centro de Biología Molecular Severo Ochoa (CSIC-UAM)

description: Total RNA from CD8 Single Positive stage (CD8SP, CD4- CD8+ CD3+ TCRαβ+) isolated from human postnatal thymus. Healthy donor 3 of 3.

hyb_protocol: Labeled targets from 5 μg of total RNA was used for hybridization on each OSU-CCC miRNA microarray custom version 4, containing 393 mouse, 409 humans and 962 ultraconserved sequences in quadruplicate. All probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6× SSPE (0.9 M sodium chloride/60 mM sodium phosphate/8 mM EDTA, pH 7.4)/30% formamide at 25°C for 18 h, washed in 0.75× TNT (Tris·HCl/sodium chloride/Tween 20) at 37°C for 40 min, and processed by using direct detection of the biotin-containing transcripts by Streptavidin-Alexa647 conjugate.

scan_protocol: Processed slides were scanned by using a Gene Pix 4000B scanner, with the laser set to 635 nm, at power 100 and PMT 80 settings.

data_processing:
Microarray images were analyzed using GenePix Pro 6.0.1.00 (Axon Instruments, Molecular Devices). Average values of the replicate spots of each miRNA were background subtracted; log2-transformed, and normalized using quantiles normalization (Bioconductor). miRNAs were retained when present in at least 20% of samples. All the data analyses were performed using BRB-ArrayTools, v3.6.0, and R v2.3.1 (R Foundation for Statistical Computing) with a P-value <0.05.
The *txt files contain normalized signal intensity

label: Biotin

source_name: postnatal thymus

label_protocol: Five micrograms of the test RNAs were labeled with 3′-(N)8-(A)12-biotin-(A)12-biotin-5′] oligonucleotide primer using the SuperScript II RNase H Reverse Transcriptase KIT (Invitrogen).

growth_protocol: Human primary thymocyte populations were purified from fresh pediatric thymus samples (aged 1 month to 4 years) by density centrifugation (Lymphoprep, STEM CELL Technologies), followed by sequential immunomagnetic selection based on cell surface markers (Dynal, Invitrogen and Miltenyi Biotec).

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen). RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: thymus

tag: t-cell developmental stage


title: NSCs, L4

value: Low cell packing density


title: Healthy donor 3 P6528 CD4SP

description: Total RNA from CD4 Single Positive stage (CD4SP, CD4+ CD8- CD3+ TCRαβ+) isolated from human postnatal thymus. Healthy donor 3 of 3.


title: sgZBTB11 #2 DOX, 1 day, Rep1

description: Library name: D1_sg6_dox_1

value: MIA PaCa-2

value: PDAC


title: S461588_WTA_007

value: Negative control


title: sgZBTB11 #2 DMSO, 1 day, Rep3

description: Library name: D1_sg6_dmso_3

value: sgZBTB11 #2 DMSO, 1 day


title: S461588_WTA_008


title: Healthy donor 3 P6526 DPCD3-

description: Total RNA from Double Positive CD3- stage (DPCD3-, CD4+ CD8+ CD3- TCRαβ-) isolated from human postnatal thymus. Healthy donor 3 of 3.


title: S461588_WTA_006


title: Healthy donor 3 P6525 DPPRETCR

description: Total RNA from Double Positive PRE-TCR stage (DPPRETCR, CD4+ CD8+ CD3lo TCRαβ-) isolated from human postnatal thymus. Healthy donor 3 of 3.


title: sgZBTB11 #2 DMSO, 1 day, Rep2

description: Library name: D1_sg6_dmso_2


title: E10.5_cut_0hpa_1

value: post-amputation flank tissue


title: NSCs, L3

value: Sprague-Dawley


title: NSCs, L2


title: S461588_WTA_005

value: Moderate


title: NSCs, M3

value: Medium cell packing density


title: E10.5_cut_1hpa_2


title: Healthy donor 3 P6524 CD4ISP

description: Total RNA from CD4 Immature single positive stage (CD4ISP, CD4+ CD1a+ CD8- CD3- TCRαβ-) isolated from human postnatal thymus. Healthy donor 3 of 3.


title: sgZBTB11 #2 DMSO, 1 day, Rep1

description: Library name: D1_sg6_dmso_1


title: S461588_WTA_004

value: Plaque


title: sgZBTB11 #2 DOX, 1 day, Rep3

description: Library name: D1_sg6_dox_3

value: sgZBTB11 #2 DOX, 1 day


title: sgZBTB11 #1 DOX, 1 day, Rep3

description: Library name: D1_sg5_dox_3

value: sgZBTB11 #1 DOX, 1 day


title: Healthy donor 3 P6523 PRET

description: Total RNA from Pre T stage (PRET, CD34+ CD1a+ CD4- CD8- CD3- TCRαβ-) isolated from human postnatal thymus. Healthy donor 3 of 3.


title: sgZBTB11 #1 DOX, 1 day, Rep2

description: Library name: D1_sg5_dox_2


title: S461588_WTA_003

value: coronary artery


title: Healthy donor 3 P6521 ETP

description: Total RNA from Early Thymic Progenitors (ETP, CD34hi CD1a- CD4- CD8- CD3- TCRαβ-) isolated from human postnatal thymus. Healthy donor 3 of 3.


title: rat_F_HiC

city: Portland

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

institute: Oregon Health and Science University

description: Library name: rat-hic-2

data_processing:
HiC data were subject to quality control and alignment with bowtie2 using the HiCUP pipeline.
Bam files were paired and converted to .cool format using cooltools.
TADs were called using HicExplorer, HicFindTADs with parameters --minDepth 100000, --maxDepth 600000, --delta 0.01, --correctForMultipleTesting fdr
Assembly: Rn6
Supplementary files format and content: BED files with TAD boundary positions

source_name: Liver

extract_protocol:
We used the Arima HiC kit to process the samples. Briefly, frozen tissue was lysed and conditioned before chromatin digestion. The digested chromatin was then filled in and biotinylated before ligation. Next, chromatin was protein-digested and reverse crosslinking overnight, followed by purification. The purified DNA was then sonicated using the bioruptor pico (Diagenode) and size selected before library preparation using the NEB DNA Ultra II, following Arima’s protocol.
The Hi-C DNA was bound to streptavidin beads before enzymatic end prep, adaptor ligation, DNA release by heat incubation, and lastly, PCR to barcode and amplify the libraries.

value: Liver


title: rat_M_HiC

description: Library name: rat-hic-1


title: S461588_WTA_002

value: Adventitia


title: sgZBTB11 #1 DOX, 1 day, Rep1

description: Library name: D1_sg5_dox_1


title: Toxoplasma and HFF, ribosome footprinting, replicate 2

city: Cambridge

first: Sebastian

last: Lourido

address: 455 Main Street

institute: Whitehead Institute

description: Library name: ribosome_footprints_rep2

library_source: other

data_processing:
Reads from both sequencing runs were treated as single-end for compatibility. Adapters were trimmed with cutadapt (v3.7) and options -u 4 -a NNNNCTGTCTCTTATACACATCTCCGAGC --match-read-wildcards --minimum-length=15 and --nextseq-trim=20 or -q 20 for NovaSeq and HiSeq reads, respectively.
STAR (v2.7.1a) was used to map reads to a metagenome of T. gondii, H. sapiens, size markers, and spike-in sequences with settings --outFilterType BySJout --outSAMattributes All --alignIntronMax 25000 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1.
A custom Toxoplasma transcriptome annotation was generated to include representative 5′ UTR isoforms expressed in our data. For ToxoDB, Markus et al. 2021 Tz TSS and Bz TSS transcript isoforms, 5′ UTRs were split into windows of three nt with bedtools makewindows, and total RNA coverage was calculated across these windows for each model using bedtools coverage -counts -s. We calculated cumulative read coverage and D for each model, where D is the ks.test statistic from comparison of a normalized, even distribution against read coverage for the model normalized to the UTR length and total cumulative sum. D values were compared for all models for a given gene, and the model with the lowest D value was selected as the representative isoform, except in the following cases: 1) In cases where the difference between D values was less than 0.05, we selected the model with the longest length. 2) In cases where all models had a D value greater than 0.4, the result was deemed inconclusive, and the 5′ UTR was excluded from further analyses. RPKM was calculated from counts generated with featureCounts, and transcripts with RPKM > 5 in both replicates were considered expressed. CDS and 3′ UTR annotations were used directly from ToxoDB models. In cases where there are multiple annotated CDS isoforms, the longest isoform was selected. The GFF file was updated with the new UTRs.
For the H. sapiens transcriptome annotation, canonical transcripts were identified from the UCSC genome browser knownCanonical option, and the H. sapiens transcriptome was filtered to include just the canonical transcript for each gene. The transcript with the longest CDS was selected for genes with multiple canonical transcripts or no canonical transcripts.
The spliced transcriptome fasta for Toxoplasma was created using gffread -w. Genome-aligned reads were re-aligned to spliced H. sapiens and T. gondii transcriptomes with STAR options --outFilterMismatchNmax 2 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate.
Total mRNA and ribosome footprint reads mapping to the CDS of each transcript, excluding the first and last three codons, were counted with featureCounts and parameters GTF.featureType="CDS", useMetaFeatures=F, readShiftType = "downstream", readShiftSize = 12, read2pos = 5, strandSpecific = 1. Ribosome footprint and mRNA RPKM were calculated for each gene using DESeq2, and translation efficiency (ribosome footprint RPKM / mRNA RPKM) was calculated for each biological replicate and the average taken.
Assembly: ToxoDB Release 68 and HostDB Release 68
Supplementary files format and content: CDS_raw_counts.xlsx is an Excel spreadsheet that contains CDS counts (excluding the first and last 3 codons) generated with featureCounts. One tab contains Toxoplasma data and one tab contains host cell data.
Supplementary files format and content: RPKM_and_TE.xlsx is an Excel spreadsheet that contains RPKM values for the CDS of each transcript, and a separate tab with translation efficiency (TE). Separate tabs are provided for Toxoplasma and host data.
Supplementary files format and content: Toxoplasma_gondii_ME49_updated_5UTRs.gff is the GFF that contains updated 5' UTR models and remaning gene annotations from ToxoDB.
Library strategy: Ribo-Seq

molecule: other

organism:
Toxoplasma gondii
Homo sapiens

source_name: T gondii: ME49, H sapiens: human foreskin fibroblast

growth_protocol: T. gondii were grown in human foreskin fibroblasts (HFFs) at 37°C and 5% CO2 and maintained in DMEM supplemented with 3% heat-inactivated fetal bovine serum and 10 ug/mL gentamicin.

extract_protocol:
Dishes of HFFs with intracellular tachyzoites were placed on ice, and washed with ice-cold PBS with 100 ug/mL cycloheximide twice. 1 mL lysis buffer (20 mM HEPES pH 7.5, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100, 2 mM DTT, 100 ug mL-1 cycloheximide, 500 U mL-1 RNaseIn Plus (Promega), and cOmplete Protease Inhibitor Cocktail (1 tablet per 10 mL buffer, Roche)) was added, and a cell lifter was used to dissociate HFFs with intracellular parasites from the dish, combining both dishes into the 1 mL sample. Lysates were passed through a 27-gauge needle 3 times, then 30-gauge needle 3 times, before incubating on ice for 5-10 minutes. Debris was pelleted by centrifugation at 4°C 1300xg for 10 minutes, and supernatant was transferred to fresh tubes. Samples were flash-frozen in liquid nitrogen and stored at -80°C.
For ribosome profiling, RNase I (Thermo Fisher) concentration was empirically tested, after which 40 U per 1 OD260 was used. Sucrose gradient preparation, fractionation, collection of 80S ribosomes, and RNA fragment purification were performed as described in Xiang and Bartel 2021. For matched RNA-seq, probes for depletion of Toxoplasma rRNAs from total RNA samples were designed through NEB, and an equal ratio of human and Toxoplasma probes (2 uL each per reaction) were used for rRNA depletion with the NEBNext rRNA Depletion Kit (Human/Mouse/Rat, NEB, E6310L). Spike-in of GFP, Renilla luciferase, and Firefly luciferase mRNAs were added to the total RNA samples. Total RNA was fragmented with RNA Fragmentation Buffer (2 mM EDTA, 12 mM Na2CO3, 88 mM NaHCO3) by incubating at 95°C for 20 minutes followed by ethanol precipitation. Ribosome footprint and total RNA libraries were processed in parallel according to an established protocol (Subtelny et. al 2014).

value: T gondii:ME49, H sapiens:human foreskin fibroblast

value: T gondii:ME49/dKu80/dHXGPRT/TIR1


title: Healthy donor 2 P6519 CD4SP

description: Total RNA from CD4 Single Positive stage (CD4SP, CD4+ CD8- CD3+ TCRαβ+) isolated from human postnatal thymus. Healthy donor 2 of 3.

value: thymus


title: sgZBTB11 #1 DMSO, 1 day, Rep3

description: Library name: D1_sg5_dmso_3

data_processing:
Data was processed using nf-core rnaseq pipeline version 3.17.0 (star_rsem) using human genome version GRCh38.p14 and Gencode annotations versions 47.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited table of counts and transcripts-per-million (TPM)

value: MIA PaCa-2

value: sgZBTB11 #1 DMSO, 1 day