Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CRISPR interference screens in ALK+ anaplastic large cell lymphoma cell culture (SU-DHL-1) under treatment with therapies used in peripheral T-cell lymphoma treatment

ABSTRACT: The following are raw Illumina sequencing files for 14-day genome-wide CRISPR interference screens conducted in a T-cell lymphoma cell culture. This submission contains the results of two sets of genome-wide screens conducted at the University of North Carolina at Chapel Hill School of Medicine, in the lab of Adam Palmer. SU-DHL-1 cells stably expressing dCas9-KRAB (Addgene # 110820) were transduced with pCRISPRi-v2 genome-wide library (Addgene #84832) and treated for 14-days with either pralatrexate, romidepsin, oxaliplatin, gemcitabine, or bortezomib. Deposited here are the raw high-throughput sequencing files, and the processed gene tables with phenotype scores, generated using the CRISPR interference screen data analysis pipeline originally published by Max Horlbeck from the lab of Jonathan Weissman.

ORGANISM(S): Homo sapiens

PROVIDER: GSE330619 | GEO | 2026/05/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome wide CRISPR screen for Trametinib sensitivity in resistant MOLM13 cells using Y. Kosuke library

Project description:Cas9-expressing trametinib resistant MOLM-13 cell lines (TM1) were generated using the Cas9-Blst (Addgene, #52962) and expanded for genome-wide loss-of-function screens using the Y. Kosuke library (Addgene, #67989) Following transduction, cells cultured in the presence of trametinib (100 nM) or DMSO after lentiviral infection.

2024-02-22 | GSE235183 | GEO

Prospective Collection of PillCam SB3 Videos and Raw Data Files for Future Developments (SODA)

Project description:Observational, Multicenter, Post-market, Minimal risk, Prospective data collection of PillCam SB3 videos (including PillCam reports) and raw data files and optional collection of Eneteroscopy reports

| 2291850 | ecrin-mdr-crc

The natural diversity of the yeast proteome links aneuploidy tolerance to genome-wide proteome

Project description:Recent advancements in genome sequencing have facilitated accessing the natural genetic diversity of species, unveiling hidden genetic traits, clarifying gene functions, and the degree to which laboratory studies can be generalized. One notable discovery is the frequent (~20%) aneuploidy - an imbalance in chromosome copy numbers - in natural Saccharomyces cerevisiae (Sc) isolates, despite the significant fitness costs and transient nature reported for lab-engineered yeast aneuploids. To examine this discrepancy, we adapted a high-throughput proteomic platform to analyze the proteome of 800 diverse yeast isolates. Matching these proteomes to the natural isolates’ genomes, transcriptomes, as well as generating ubiquitinome and protein turnover data for selected isolates, we report that natural and lab-generated aneuploids differ specifically at the proteome. While lab-generated aneuploids attenuate specific proteins – mostly protein complex subunits – and do not alter the average gene dosage provided by chromosome duplications, in natural strains, 70% of proteins encoded on aneuploid chromosomes are attenuated, and protein levels are shifted towards the euploid state chromosome-wide. Our data links chromosome-wide dosage compensation in natural strains to i) genome-wide buffering of gene expression changes manifesting in trans on euploid chromosomes, ii) increased expression of structural components of the ubiquitin proteasome system, and iii) increased global rates of protein turnover. Our results encourage the exploitation of natural diversity of species to understand complex biological processes at the molecular level. This submission contains the raw files for the disomics lab engineered strains, the library used for the analysis and the corresponding DIA-NN report and associated files.

2024-03-11 | PXD044526 | Pride

DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics

Project description:This dataset consists of 44 raw MS files, comprising 27 DIA (SWATH) and 15 DDA runs on a TripleTOF 5600 and of two raw mass spectrometry files acquired on a Q Exactive. The composition of the dataset is described in the manuscript by Tsou et al., titled: "DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics", Nature Methods, in press Raw files are deposited here in ProteomeXchange and are associated with the DIA-Umpire processed data. All DIA-Umpire processed results for each sample together with DDA results are deposited in separated folders. Also see the "DataSampleID.xlsx" associated with this Readme file. Internal reference from the Gingras lab ProHits implementation: Project 94, Export version VS2 (Tsou_DIA-Umpire)

2015-01-21 | PXD001587 | Pride

CRISPR-MIP replaces PCR and reveals GC and oversampling bias in pooled CRISPR screens

Project description:This is data for the evaluation of a new way of counting sgRNAs in CRISPR screens using padlock probes and UMIs. It is compared to the typical PCR-based approach. In particular, a dropout screen was performed in MiaPaCa-2 cells using the Human Kinome CRISPR pooled library (Addgene #75314)

2024-08-18 | E-MTAB-14379 | biostudies-arrayexpress

EpiMatch DNA Methylation Resource

Project description:Genome-wide DNA Methylation Data from Illumina HumanMethylationEPIC arrays for whole blood samples from 570 healthy individuals. Raw IDAT files are available for a subset of 403 samples on EGA. Raw data (IDAT files) and associated phenotype information are available for all individuals included in this study (n=570) directly from CIBMTR. Data are available under controlled access release upon reasonable request and execution of a data use agreement. Requests should be submitted to CIBMTR at info-request@mcw.edu and include the study reference IB17-04.

2022-04-25 | GSE196696 | GEO

Response to CBF2 expression

Project description:This experiment was annotated by TAIR (http://arabidopsis.org). This experiment looks at changes in gene expression in response to constitutive expression of the transcription factor CBF2. Experimenter name = Jonathan Vogel Experimenter phone = 517-355-2299 Experimenter fax = 517-353-5174 Experimenter department = MSU-DOE Plant Research Lab Experimenter institute = Michigan State University Experimenter address = East Lansing Experimenter zip/postal_code = MI 48824 Experimenter country = USA Keywords: genetic_modification_design

2006-08-15 | GSE5536 | GEO

Response to ZAT12 expression

Project description:This experiment was annotated by TAIR (http://arabidopsis.org). This experiment looks at changes in gene expression in response to constitutive expression of the transcription factor ZAT12. Experimenter name = Jonathan Vogel Experimenter phone = 517-355-2299 Experimenter fax = 517-353-5174 Experimenter department = MSU-DOE Plant Research Lab Experimenter institute = Michigan State University Experimenter address = East Lansing Experimenter zip/postal_code = MI 48824 Experimenter country = USA Keywords: genetic_modification_design

2007-01-08 | GSE5742 | GEO

Response to cold, plate grown plants

Project description:This experiment was annotated by TAIR (http://arabidopsis.org). This experiment looks at changes in gene expression in Col-0 plants grown in plates in response to low temperature over time. Experimenter name = Jonathan Vogel Experimenter phone = 517-355-2299 Experimenter fax = 517-353-5174 Experimenter department = MSU-DOE Plant Research Lab Experimenter institute = Michigan State University Experimenter address = East Lansing Experimenter zip/postal_code = MI 48824 Experimenter country = USA Keywords: time_series_design

2006-08-15 | GSE5534 | GEO

Response to cold, soil grown plants

Project description:This experiment was annotated by TAIR (http://arabidopsis.org). This experiment looks at changes in gene expression in Col-0 plants grown in soil in response to low temperature over time. Experimenter name = Jonathan Vogel Experimenter phone = 517-355-2299 Experimenter fax = 517-353-5174 Experimenter department = MSU-DOE Plant Research Lab Experimenter institute = Michigan State University Experimenter address = East Lansing Experimenter zip/postal_code = MI 48824 Experimenter country = USA Keywords: time_series_design

2006-08-15 | GSE5535 | 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