Sf21 RNAseq reads
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ABSTRACT:
PROVIDER: PRJEB24631 | ENA |
REPOSITORIES: ENA
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Project description:RNA extracted from Tni cell line (High Five) were sequenced and used in genome annotation worflow.
| PRJEB24632 | ENA
Project description:Total RNA extracted from the head and neck cell line CAL165 were purified using miRNeasy minikit (Qiagen). RNA libraries were then generated with the NEB next small library prep set for SOLID (New England Biolabs) and sequenced on the Applied Biosystems SOLiD 5500 wildfire system following the manufacturer's instructions.
2017-06-07 | GSE89510 | GEO
Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
| 2612481 | ecrin-mdr-crc
Project description:Abstract: The Kinetoplastida (Euglenozoa) are unicellular flagellates that include the trypanosomatid parasites, most notably Trypanosoma brucei, T.cruzi and Leishmania spp. These organisms cause substantial mortality and morbidity in humans and their livestock worldwide as the causative agents of African sleeping sickness, Chagas disease and leishmaniasis respectively. Draft genome sequences are available for several species of both Trypanosoma and Leishmania. Bodo saltans is a free-living heterotroph found worldwide in freshwater and marine habitats, and it is among the closest bodonid relatives of the trypanosomatids. The purpose of a B. saltans genome sequence is to provide an 'out-group' for comparative genomic analysis of the trypanosomatid parasites. It will provide a model of the ancestral trypanosomatid to distinguish those derived parts of the parasite genomes (i.e., unique trypanosomatid adaptations) from those which are a legacy of the free-living ancestor. To aid annotation of the B.saltans genome sequence, total genomic RNA was extracted on four occasions from the total cellular mass of 160ml of B.saltans cell culture, for the purposes of transcription profiling by high throughput sequencing. Cells were unmodified. B.saltans cells were grown in water at 4oC. Total genomic RNA was extracted from a cell pellet using TRIZOL reagent and ethanol precipitated. Poly A+ mRNA was purified from total RNA using oligo dT dyna bead selection and libraries were created using the Illumina RNA-seq protocol. The samples were sequenced on an Illumina HiSeq 2000. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2012-07-13 | E-ERAD-88 | biostudies-arrayexpress
Project description:M238P BRAFV600E mutant melanoma cells sensitive to the BRAF inhibitor Vemurafenib (PLX4032) and the corresponding resistant M238R cell line were cultured in standard conditions. RNA samples were then harvested and sequenced with the Nanopore long-reads protocol.
2021-12-29 | GSE171882 | GEO
Project description:Bicyclus anynana butterflies were reared at 17°C and 27°C to produce the dry and wet season forms. RNA was extracted using TRIzol from the heads of 12 individual animals ~0-3 hours after eclosing; 3 dry season females, 3 wet season females, 3 dry season males, and 3 wet season males. A TruSeq RNA Sample Preparation Kit v2 was used to make 12 double stranded cDNA libraries from polyadenylated RNA. We size selected for DNA at ~280-340 bp. Libraries were sequenced using a HiSeq 2500, paired end 100-cycle sequence run.
2015-10-01 | E-MTAB-3887 | biostudies-arrayexpress
Project description:RNA-seq analysis of Drosophila pharate adults Total RNA extracted from four lines of Drosophila melanogaster pharate adults were depleted of ribosomal RNAs and sequenced.
2014-04-22 | E-GEOD-50711 | biostudies-arrayexpress
Project description:To know BRs was how to cause transgenic line L100 leaves changed, we took the sixth leaves of transgenic line L100 to RNA-seq sequence. Total RNA was extracted from the sixth leaves of six-leaf stage of transgenic line L100 and wild type Q319. cDNA library was builded in the BIOMARKER, 100.20M original reads were sequenced based on Illumina HiSeq2000, and through rRNA, low quality fragment DNA of filtering, ultimately, we obtained 69.01M high quality clean reads. Compared with reference gene sequence(AGPv3), according to genes function annotation, we found 201 different expression genes. We classified the different expression genes according to Cellular Component, Molecular Function and Biological Process. It showed that BRs could affect many genes expression involved in different biological process.
2018-12-27 | GSE108627 | GEO
Project description:RNA from Xiphophorus maculatus (X. maculatus) are isolated and sequenced for annotation of enhanced X. maculatus genome
2017-11-28 | GSE107449 | GEO
Project description:Medulloblastoma is subdivided into different subgroups: WNt, SHH, Group 3 and Group 4. Since these subgroups are associated with different OS and metastasis rates it is crucial to understand them better. Six medulloblastoma cell lines, DAOY, ONS-76, D458, HD-MB03, CHLA-01-MED, CHLA-01R-MED, have been sequenced to compare them with medulloblastoma patient data. Methods: Medulloblastoma cell lines representating the different subgroups have been cultured and cell were harvested and RNA was isolated when 70% confluency was reached. In detail, DAOY and D458 were grown in DMEM (Thermo Fisher) with 10% FBS (HyClone, Thermo Fisher), ONS-76 and HD-MB03 were grown in RPMI 1640 (Sigma-Aldrich) with 10% FBS and CHLA-01-MED and CHLA-01R-MED were grown in DMEMF12 supplemented with B27, 20 ng/ml EGF and 20 ng/ml bFGF (all Thermo Fisher). All cells were maintained at 37 °C in a humidified atmosphere containing 5% CO2. During the course of this study, all cell lines were routinely confirmed to be mycoplasma negative (MycoAlert, Lonza, Basel, Switzerland).Cell pellets of at least 100,000 cells were washed with HBSS and frozen in liquid nitrogen. For homogenization, ceramic spheres (Lysing Matrix D, MP Biomedicals, Santa Ana, California, USA) and the FastPrep-24 homogenizer was used (MP Biomedicals, speed 4 m/s, tube holder MP:24*2 and time 20 s). Total RNA was isolated from 2D pellets using the NucleoSpin RNA Plus Kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions. In total, 3 biological replicates of each cell line were processed respectively. RNA amount was determined using the Qubit RNA BR kit with the Qubit 4 (both ThermoFisher). Library preparation and RNA sequencing (transcriptome sequencing including lncRNA on Illumina PE150) were performed by Novogene (Cambridge, UK) Company Limited, Cambridge, UK. Samples with less than 100 ng or with non-qualifying RIN values were excluded from the sequencing. All prepared libraries successfully passed Novogene’s internal quality control checks and were sequenced. Following sequencing, quality control of the sequencing data was performed that confirmed all samples had high quality scores, indicating good technical performance of the sequencing. We used FastQC to perform quality checks of raw RNA data followed by adapter and low quality read filtering using the Cutadapt package (version 1.16.6) [reference]. The trimmed paired-end sequences were aligned with the human genome (hg38) and Gencode annotation (v35) using the STAR (version 2.7.5b) alignment tool. Unique reads from genomic alignment were processed and we used the featureCount tool for transcript abundance quantification. STAR read counts were used as input into edgeR. Genes with read counts greater than 10 in three or more samples were kept for subsequent analyses. After normalization analyses, counts per million (cpm) on a log2 scale were used for downstream exploratory analyses.
2022-03-02 | E-MTAB-9823 | biostudies-arrayexpress