Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

2126f067-dc14-4271-9adf-21a30ba15e14 - samples

ABSTRACT: This dataset contains raw fastq files from the RNA-Seq of 96 T-Acute Lymphoblastic Leukemia. Libraries where prepared using Agilent SureSelect XT-HS2 RNA Reagent Kit. As such, reads contain molecular barcodes that could be specifically handled using the AGeNT tool.

PROVIDER: EGAD00001010273 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Single cell RNA-sequencing of Spike-ins and mESC using Smart-Seq2 on 96-well plates

Project description:In this study, we assess technical differences between commonly used single-cell RNA-Sequencing (scRNA-Seq) methods. We perform scRNA-seq on a homogenous population of mouse embryonic stem cells along with two kinds of control spike-in molecules to assess sensitivity and accuracy of these specific methods. In this dataset, we assess the RNA-degradation and decay rates by subjecting both spike-in molecules to range of repeated freezing and thawing (freeze-thaw) cycles. We manually add spike-in molecules across a 96-well plate (containing cells and reagents), perform Smart-Seq2 method manually and generate single-cell libraries using Nextera XT kit

2017-03-14 | E-MTAB-5481 | biostudies-arrayexpress

p62/SQSTM1 iCLIP in Human Huh-7 cells

Project description:These are the results of the iCLIP experiment for p62/SQSTM1 in Human Huh-7 cells treated with DMSO. We used iCLIP method to identify the RNA targets of p62 and nucleotide positions of the p62 interaction on RNA. We used 2 replicates and 2 different antibodies against endogenous p62 to enrich protein/RNA complexes. cDNAs were tagged with iCLIP composite barcodes (e.g. NNNTTGTNN) which contain 4 sample-encoding bases (e.g. TTGT) and and 5 random bases (noted with N in NNNTTGTNN example) which serve as unique molecular identifiers to post-filter PCR duplicates. These composite barcodes are found in the read headers (after last colon ':' character) of submitted fastq files.

2018-03-31 | E-MTAB-4894 | biostudies-arrayexpress

62e9d930-2194-4e13-b6c0-db0b38382413 - samples

Project description:Whole exome sequencing (WES) libraries were prepared from 200ng of genomic DNA using the Agilent SureSelect XT Target Enrichment System for Illumina Paired-End Multiplexed Sequencing Library coupled with the Agilent SureSelect XT Human all exon v6 capture reagent. Libraries were sequenced on a NextSeq 550 sequencer using the High output 300 cycles kit generating 150bp paired end single-indexed reads. Alignment against b37 using Novoalign (version 3.02.08).

| EGAD00001004539 | EGA

Tissue Specimens from Patients with Melanoma for Genetic Analysis

Project description:<p>The purpose of this study was to obtain tissue specimens derived from patients with melanoma to generate research tools to advance our understanding of the genetics, pathogenesis, and therapeutics of melanoma. Briefly, tissue was obtained from metastatic lesions and used to generate clonal primary cell lines from melanoma cells and fibroblasts from the tumor microenvironment. RNA was extracted from low passage cell lines using Trizol reagent. cDNA libraries were prepared using the TruSeq mRNA sample preparation kit, v2 (Illumina) and sequenced on the HiSeq 2000 platform (Illumina). The submitted files are bam files that contain both unaligned and aligned reads (human genome, build hg19). </p>

| phs001115 | dbGaP

Homo sapiens

Project description:Multiplexing droplet-based single cell RNA-sequencing using genetic barcodes

| PRJNA381100 | ENA

SSN-seq: Multiplexed single-cell transcriptomic profiling via genetic barcoding with shielded small nucleotides

Project description:To facilitate scalable longitudinal profiling of single cells we developed a universal permanent genetic cell barcoding technology based on the expression of shielded small nucleotides coupled with single-cell RNA-seq (SSN-seq). SSN barcodes are highly expressed and contain direct-capture sequences to enable recovery of distinct barcodes directly in each single-cell transcriptome allowing cell identity history to be recorded over time, in parallel with cell identity. SSN-seq is compatible with both 3’ and 5’ single-cell profiling and is readily adaptable to numerous cell types including human primary T cells and CAR T cells making it a promising tool for rapidly improving adoptive cell therapies and expanding their functionality. We applied SSN-seq to track the dynamics of CAR T cell states at the time of infusion and upon isolation from in vivo tumor rechallenge model. Our study identified that a novel combination of cytokines and small molecule inhibitors used for CAR T cells manufactured ex vivo, promotes the expansion of persistent CD4+ memory T cell populations in vivo. Together, these results demonstrate the utility of our method for multiplexed perturbation experiments that reveal the dynamics of cell states over time, with a high degree of confidence.

2023-07-31 | GSE201647 | GEO

RNA sequencing of primary isolated unstimulated murine splenic DC1 and DC2 from specific pathogen free (SPF), Germ free (GF) and Interferon alpha/beta receptor 1 (Ifnar) knock out mice

Project description:The transcriptomes of primary isolated unstimulated murine splenic cDC1 and cDC2 from specific pathogen free (SPF) were compared to cDC1 and cDC2 from Germ Free (GF) and Interferon alpha/beta receptor 1 (Ifnar) knock out mice. Total RNA was prepared from sort-purified cDC1 and cDC2 (for each sample 3 individual mice were pooled) using Trizol reagent (Invitrogen) in combination with the miRNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions. For poly-A-dependent cDNA synthesis and a first amplification step 10 ng of total RNA was used as input in the Smart-Seq v4 mRNA Ultra Low Input RNA Kit (Clontech) and processed according to the manufacturer’s instructions. 1 ng of the purified cDNA was used for tagmentation and library completion with the Nextera XT library preparation kit (Illumina). In the following, 2x75nt paired-end sequencing was performed on a NextSeq 500.

2020-03-30 | E-MTAB-8883 | biostudies-arrayexpress

ZipSeq : Barcoding for Real-time Mapping of Single Cell Transcriptomes

Project description:single cell RNA Sequencing runs for various models linking transcriptomes with regional position using spatially printed barcodes

2020-06-01 | GSE145502 | GEO

Genome-Wide Identification of ABA Responsive microRNAs in the Root of Populus euphratica

Project description:More then 10 million raw reads were acquired. In total, 238 unique mature sequences which contain 142 conserved miRNA and 96 novel miRNAs were identified.

2018-12-01 | GSE107802 | GEO

Microarray analysis of V. cholerae genes differentially expressed in 8h rabbit ileal loop fluid.

Project description:Transcriptional analysis of wild-type V. cholerae isolated from the rabbit ileal loop was performed by quickly pelleting bacteria from the fluid accumulated in the ileal loops after 8 h of infection. The bacteria were then resuspended in Trizol reagent and frozen on dry ice. The wild-type bacteria from three independent experiments in three different rabbits were analyzed. RNA was isolated from the Trizol agent, treated with DNaseI (Ambion, Austin, Texas, United States), and cleaned by using the RNeasy kit (Qiagen, Valencia, California, United States).

2010-09-29 | GSE24407 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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