453c33fc-c2f0-4cbe-945b-09c3697f6e24 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001004276 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:The study included 15 patients (7 males, 8 females) with JMML. Peripheral blood and/or bone marrow aspirates were collected on EDTA at diagnosis. Non-hematopoietic tissues (fibroblasts) was derived from skin biopsy for each patient. Exome sequencing was performed in several distinct series between 2012 and 2017, which explains the differences in capture kit versions and reference genome version.Targeted enrichment and massive parallel sequencing were performed on paired genomic DNA from leukocytes and fibroblasts. Exome capture was carried out using the SureSelect Human All Exon V4+UTRs or V5 or V5+UTRs or SureSelect Clinical Research (Agilent Technologies, Santa Clara, CA, USA) according to manufacturer’s instruction and protocols by IntegraGen (Evry, France). Paired-end 75 bases sequencing was performed on a HiSeq2000 or HiSeq4000 instrument (Illumina, San Diego, CA, USA). Image analysis and base calling were performed using the Real Time Analysis (RTA) pipeline v. 1.14 (Illumina) with default parameters. The alignment of paired-end reads to the reference human genome (UCSC GRCh37/hg19 or UCSC GRCh38), variant calling and generation of Quality variants scores were carried out using the CASAVA v.1.8 pipeline (Illumina).
2018-03-14 | E-MTAB-6461 | biostudies-arrayexpress
Project description:Total RNA was extracted from Lin-Sca-1+c-Kit+ (LSK) cells sorted from the BM of Spred1HSCΔ/ΔSCLtTA/BCR-ABL (HSC KO) and Spred1HSCwt/wtSCLtTA/BCR-ABL (HSC wt) (n=5 mice per group, both group given 7 doses of 250μg poly(I:C), ip, every two days, to activate Mx1-cre), Spred1ECΔ/ΔSCLtTA/BCR-ABL (EC KO) and Spred1ECwt/wtSCLtTA/BCR-ABL (EC wt) (n=5 mice per group) mice using the miRNeasy micro Kit (Qiagen, Valencia, CA). SMART-Seq® Ultra Low Input RNA Kit for Sequencing – v4 (TaKaRa, Cat 634888) was used for generating amplified double stranded (ds) cDNA from each sample with 2ng of input total RNA according to the manufacturer's protocol. The resulting ds cDNA was sheared with Covaris LE220 with the setting of DNA fragment size of 200bp peak. The sheared DNA was used for sequencing library preparation by using KAPA HyperPrep Kits (Roche, Cat KK8500). The final libraries were quantified with qubit and bioanalyzer. The sequencing was performed with the single read mode of 51 cycles of read1 and 7 cycles of index read with V4 reagents on Illumina Hiseq2500. Real-time analysis (RTA) 2.2.38 software was used to process the image analysis and base calling. The nf-core RNAseq pipeline v1.3 was used to process the raw sequencing reads (https://nf-co.re). RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic3 and polyA tails using FASTP4. The processed reads were mapped back to the mouse genome (mm10) using STAR software (v. 020201)5. The HTSeq software (v.0.6.0)6 was applied to generate the count matrix, with default parameters. Differential expression analysis was conducted by adjusting read counts to normalized expression values using TMM normalization method in R7. Briefly, for each comparison between HSC KO LSKs and HSC wt LSKs and between EC KO LSKs and EC wt LSKs, general linear models were applied to identify DEGs using TMM normalization expression level as depending variable, and genotype as independent variable. Genes with a p-value less than 0.05 and with a fold change (FC) greater than 1.5 or less than 0.7 were considered as significant up- and down-regulated genes, respectively. Pathway analysis was conducted using GSEAPreranked algorithm using GSEA Desktop program in Java8, 9. The former requires a list of up- and down-regulated genes, while the latter a ranked list of whole genes according to their log2 fold change and p-values.
2021-09-30 | GSE181589 | GEO
Project description:We performed data preprocessing, m6A peak calling, motif analysis, meta-gene plotting, and differential RNA methylation analysis using multiple tools. Scripts are publically avalible https://github.com/abearab/imRIP.
2023-01-13 | GSE222824 | GEO
Project description:We examined the viral epitranscriptome in EBV transformed lymphoblastoid cell lines (LcLs) and EBV-positive Burkitt's lymphoma, Akata cells, using methylated RNA immunoprecipitation followed by sequencing (MeRIP-seq). Biological replicates of ribo-RNA deleted mRNA of each cell type were prepared for MeRIP-seq followed by peak calling using the exome Peak package with settings for stringent peak calling on both strands of the genome.
2023-08-12 | GSE129217 | GEO
Project description:Investigating chromatin interactions between regulatory regions such as enhancer and promoter elements is pivotal for a deeper understanding of gene expression regulation. The emerging 3D mapping technologies focusing on enriched signals such as Hi-TrAC/Trac-looping and HiChIP, compared to Hi-C, reduce the sequencing cost, and provide higher interaction resolution for cis-regulatory elements and more comprehensive information such as chromatin accessibility. A robust pipeline is needed for the comprehensive interpretation of these data, especially for loop-centric analysis. Therefore, we have developed a new versatile tool named cLoops2 for the full-stack analysis of the 3D chromatin interaction data. cLoops2 consists of core modules of peak-calling, loop-calling, differentially enriched loops calling and loops annotation. Additionally, it also contains multiple modules to carry out interaction resolution estimation, data similarity estimation, features quantification and aggregation analysis, and visualization. cLoops2 with documentation and example data are open source and freely available at GitHub: https://github.com/YaqiangCao/cLoops2
2021-11-29 | GSE179010 | GEO
Project description:Illumina HiSeq2500 technology was used to generate mRNA profiles from Phanerochaete chrysosporium treated with oak extractives for 1, 3 and 6h. 125bp pair-end reads were generated and aligned to the P.chrysosporium reference transcripts. (https://genome.jgi.doe.gov/Phchr2/Phchr2.home.html) using CLC Genomics Workbench 9.
2018-10-01 | GSE119735 | GEO
Project description:PROTEOFORMER is a pipeline for generating a search space of candidate translation products based on ribosome profiling data. The pipeline was published in 2014, but since then, several features have been added. For this project, the PROTEOFORMER pipeline 2.0 was tested on human HCT116 and Jurkat cell ribosome profiling data with all its new features and then compared to raw MS data of both cell lines, validating its use as a proteogenomic tool. In this study, results of 3 proteoform calling methods were combined (classical PROTEOFORMER proteoform calling, PRICE and SPECtre). Afterwards, results were eventually combined with the canonical or splicing-included version of human UniProt. The different described combinations were exported as a FASTA file and used as search space for searching matching MS data.
2019-05-03 | PXD011353 | Pride
Project description:RNA was isolated from siCTRL, siNSUN2 and ALYREF-RIP HeLa cells, and multiple mouse tissues using the TRIzol (Invitrogen) reagent by following the company manual. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) or HiSeq2500 in paired-read mode, creating reads with a length of 101 or 125 bp. Sequencing chemistry v2 or v4 (Illumina) was used.
2017-04-19 | GSE93750 | GEO
Project description:We performed DNase-seq on two osteosarcoma cell lines, Saos-2 and U2OS. This was done to identify regulatory regions within the genomes of these cells. We performed hotspot calling on these data using Hotspot2 (https://github.com/Altius/hotspot2) to identify 51,556 DNaseI hypersensitive sites within Saos-2 cells and 63,388 within U2OS cells.
2020-01-03 | GSE142160 | GEO