Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

WGS Genlisea

ABSTRACT: WGS to study Genome size evolution in the genus Genlisea

PROVIDER: PRJEB1866 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	ERR296825_1.fastq.gz	Fastqsanger.gz
	ERR296825_2.fastq.gz	Fastqsanger.gz
	ERR296826_1.fastq.gz	Fastqsanger.gz
	ERR296826_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

MYC drives temporal evolution of small cell lung cancer subtypes by reprogramming neuroendocrine fate [WGS data]

Project description:Distinct SCLC molecular subtypes have been defined based on expression of lineage-related transcription factors: ASCL1, NEUROD1, POU2F3 or YAP1, but their origins remain unknown. To study transcriptional dynamics of MYC-driven tumor evolution and compare transcriptional states to human SCLC tumors, we performed bulk and single-cell RNA-sequencing on various timepoints of Rb1/Trp53/MycT58A (RPM) tumor cells (from Ad-Cgrp-Cre infected mice) as they progress in culture, and on RPM bulk tumors. Here, to complement these analyses we performed ~30X whole-genome sequencing (WGS) of early (day 4) and late (day 23) time-point RPM tumor cells from culture, along with a matching normal blood control to confirm complete loss of expected regions of Rb1 and Trp53. WGS analyses revealed no detectable copy number variations (CNVs), and SNV analysis suggests that minimal clonal and subclonal evolution occurs in vitro. Together, these data ultimately reveal that MYC drives the dynamic evolution of SCLC subtypes. We find that MYC promotes a temporal shift from an ASCL1-to-NEUROD1-to-YAP1+ state from a neuroendocrine cell of origin. MYC activates Notch signaling to dedifferentiate tumor cells to non-neuroendocrine fates. These findings support our overall conclusions that genetics, cell of origin, and tumor cell plasticity determine SCLC subtype.

2020-05-28 | GSE149444 | GEO

RNA Seq Genlisea

Project description:RNA Seq to study Genome size evolution in the genus Genlisea

| PRJEB1867 | ENA

ATF4-dependent fructolysis fuels brain tumorigenesis (WGS)

Project description:The goals of WGS (Whole Genome Sequencing) analysis in TJ46 cells derived from a GBM primary tissue to obtain information on the genetic alterations that characterize this model.

2022-09-20 | GSE202644 | GEO

WGS from K562 (ENCSR053AXS)

Project description:The data contained in this Experiment come from 10X Chromium Genomics WGS of K562 cell line using the Chromium™ Genome v2 Library Kit & Gel Bead Kit For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2021-06-15 | GSE176798 | GEO

Exploring the spectrum of somatically acquired genomic lesions in HCLc by WGS

Project description:Whole genome sequencing of 10 HCLc tumor and matched-germline T cells. Genomic DNA from highly purified HCLc tumor and T cell populations were utilized for library preparation using NEBNext Ultra DNA library prep kit. Sequencing was performed as 150 bp paired end sequencing using four lanes of an Illumina HiSeq4000 to an average depth of 12X. Reads from each library were aligned to the human reference genome GRCh37 using BWA-MEM (v0.7.12). The analysis of somatic genetic alterations in WGS data from tumor-germline pair HCLc samples was divided based on the nature of the mutation, as follow: single-nucleotide variants (SNVs), indels, CNAs and SVs. Moreover, COSMIC mutational signatures and subclonal architecture was inferred for each tumor.

2023-01-01 | E-MTAB-12046 | biostudies-arrayexpress

WGS from HepG2 (ENCSR319QHO)

Project description:The data contained in this Experiment come from 10X Chromium Genomics WGS of HepG2 cell line For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2021-06-15 | GSE177129 | GEO

Profiling of Sarcomas from Archival Tissues [lp-WGS]

Project description:We performed single nuclei RNA-sequencing (snRNA-seq) with matched T cell receptor sequencing (TCR-seq), and pool matched low pass whole genome sequencing (WGS) of eight specimens from six patients, encompassing four undifferentiated polymorphic sarcomas (UPS) and four intimal sarcomas (INS), and paired specimens from two patients (one UPS and INS each) treated with immune checkpoint blockade (ICB).

2024-06-21 | GSE243377 | GEO

WGS from transverse colon (ENCSR613XEH)

Project description:The library contained in this Experiment corresponds to 10X Genomics Chromium prepared WGS. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2021-06-15 | GSE177554 | GEO

WGS from transverse colon (ENCSR997HAI)

2021-06-15 | GSE178062 | GEO

WGS from transverse colon (ENCSR456SNK)

2021-06-15 | GSE177308 | GEO