Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MRNA transcriptome sequencing of tumor bearing lungs

ABSTRACT: mRNA transcriptome sequencing of tumor bearing lungs

PROVIDER: PRJNA695255 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13562819_1.fastq.gz	Fastqsanger.gz
	SRR13562819_2.fastq.gz	Fastqsanger.gz
	SRR13562820_1.fastq.gz	Fastqsanger.gz
	SRR13562820_2.fastq.gz	Fastqsanger.gz
	SRR13562821_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 32

Similar Datasets

mRNA transcriptome sequencing of tumor bearing lungs

Project description:mRNA transcriptome sequencing of tumor bearing lungs from KrasLSL-G12D/+Lkb1fl/fl, KrasLSL-G12D/+Lkb1fl/flIl1f9-/-(KL9) and KrasLSL-G12D/+Lkb1fl/flIl1f5-/-(KL5) or KrasLSL-G12D/+Tp53fl/fl, KrasLSL-G12D/+Tp53fl/flIl1f9-/-(KP9) and KrasLSL-G12D/+Tp53fl/flIl1f5-/-(KP5) after 10 weeks Ad-cre injection Tumor-burdened lungs from KL/KL5/KL9 mice and KP/KP5/KP9 mice were perfused through alveolar lavage and cardiac lavage with PBS, dry it quickly, and then homogenized in 2 ml of TRIzol (Invitrogen). Total RNAs were prepared and the quality of RNAs was determined by agarose gel electrophoresis and spectrophotometer analysis. Poly(A) mRNA was subsequently purified from 10μg total RNA using NEBNext Oligo d(T)25 Magnetic Beads Isolation Module. First-strand complementary DNA was synthesized with NEBNext RNA First-Strand Synthesis Module. NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module was used for the synthesis of the complementary strand of first-strand cDNA. The resulting double-stranded DNA was purified and Vazyme TruePrep DNA Library Prep kit V2 was used to prepare libraries followed by sequencing on an Illumina Hiseq X Ten platform with 150-bp paired-end reads strategy (Novogene). Quality control of mRNA-seq data was performed by using Fatsqc (v0.11.9) and low-quality bases were trimmed by Trim_galore (0.6.4_dev). All RNA-seq data were mapped to the mouse genome (Mus_musculus_Ensemble_94) by Hisat2 (v.2.0.5) and allowed a maximum of two mismatches per read. Gene expression level was calculated by FeatureCounts (v.2.0.0) with default parameters and normalized by FPKM (Fragments Per Kilobase of exon model per Million mapped fragments).

2021-01-28 | GSE165640 | GEO

Characterizing Macrophage Diversity in Metastasis-Bearing Lungs Reveals a Lipid-Associated Macrophage Subset

Project description:Single cell RNA sequencing was performed on CD45+Ly6G-CD64+MerTK+ macrophages isolated from the lungs of mice 5 weeks after transplantation of 4T1-Luc mammary gland tumors. The purpose of this study was to determine the unique macrophage subsets present in the lungs of mice bearing mammary tumor metastases.

2021-08-31 | GSE164302 | GEO

Bulk RNA-Seq analysis of CD8+ T cells from treatment-naïve matched tumor-bearing lungs and spleens from the HKP1 orthotopic mouse lung adenocarcinoma model

Project description:To investigate how gene expression profiles change in CD8+ T cells based on time, tumor burden, and tissue localization, we orthotopically implanted the mouse lung adenocarcinoma HKP1 cell line expressing luciferase into syngeneic C57BL/6 mice by tail vein injections. Tumor growth was monitored by bioluminescence imaging. A separate cohort of mice received no tumor implantation. At days 7, 17, and 24 post tumor implantation, mice were euthanized and CD8+ T cells sorted from tumor-bearing lungs and spleens, or matched naive lungs and spleens. We then performed gene expression profiling analysis using data obtained from RNA-seq of sorted cells, comparing across time, tumor burden, and tissue localization.

2023-10-19 | GSE218141 | GEO

Expression data for cCD1 cell-sorted from the lungs of healthy or KP tumor-bearing mice

Project description:The goal of this study was to identify mechanism of suppression of cDC1 in a model of genetically driven lung adenocarcinoma (KP). As part of the study we analyzed the transcriptional differences between cDC1 cell-sorted from healthy lung and those cell-sorted from KP bearing lungs.

2021-03-06 | GSE119574 | GEO

Gene expression signatures for murine alveolar type II lung epithelial cells after tumor bearing

Project description:To determine the influence of primary tumors on pre-metastatic lungs, we have employed whole genome microarray expression profiling as a discovery platform to identify gene signatures of alveolar type II epithelial cells (AT-II) in TLR3 deficient mice (Tlr3-/-) and wide-type (WT) littermates with tumor bearing. We subcutaneously inoculated Tlr3-/- and WT mice with Lewis lung carcinoma (LLC). Two weeks later, lung tissues from Tlr3-/- and WT mice were dissociated and AT-II cells were sorted. AT-II cells from mice without tumor bearing were set as controls. Primary tumor induced gene expression in AT-II cells from Tlr3-/- and WT mice was measured at 2 weeks after tumor inoculation subcutaneously. AT-II cells from mice without tumor bearing were set as controls.

2016-08-10 | E-GEOD-76397 | biostudies-arrayexpress

Transcriptome of tumor tissues from MC38 bearing mice

Project description:Transcriptome of tumor tissues from MC38 bearing mice Transcriptome

| PRJNA1044251 | ENA

Expression data for cCD1 cell-sorted from the lungs of healthy or KP tumor-bearing mice

Project description:Expression data for cCD1 cell-sorted from the lungs of healthy or KP tumor-bearing mice

| PRJNA489629 | ENA

Transcriptional profiling of NK cells sorted from lungs and axillary LNs from Cdh1F/F;Trp53F/F;Foxp3GFP-DTR mice bearing 100mm2 orthotopically transplanted mammary tumors, treated with difteria toxin (DT) or PBS [NK]

Project description:We studied the impact of DT treatment (Treg depletion) on NK cells (CD3-, NKp46+, DX5+) in axillary TDLNs and lungs of tumor bearing Foxp3GFP-DTR mice . Here we generated RNAseq data from sorted NK cells from DT or PBS treated Foxp3GFP-DTR mice bearing 100mm2 mammary tumors from lungs, axillary TDLNs

2022-03-01 | GSE169025 | GEO

Transcriptional profiling of WT Tregs and Tregs sorted from K14cre;Cdh1F/F;Trp53F/F mice bearing 225mm2 mammary tumors from blood, spleen, lungs, TDLNs, tumor and healthy mammary gland [Treg]

Project description:We studied the impact of mammary tumorigenesis on Tregs in tumors and distant organs (CD3+CD4+CD25+). Here we generated RNAseq data from sorted Tregs (CD3+CD4+CD25+) from WT and K14cre;Cdh1F/F;Trp53F/F mice bearing 225mm2 mammary tumors from blood, spleen, lungs, TDLNs, tumor and healthy mammary gland

2022-03-01 | GSE169024 | GEO

Transcriptome Sequencing of Tumor-educated Lung Epithelial Cells in the Pre-metastatic Niche

Project description:We performed transcriptome sequencing on epithelial cells, isolated from lungs of normal and tumor-bearing mice, to shed light on the function and phenotype changes of lung epithelial cells in the pre-metastatic niche.

2022-07-21 | GSE195755 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data