4633742b-ae0d-459e-b79e-137c55d41caf - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001008205 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:RNA-sequencing of human hepatocellular carcinoma biopsies (n=14), 44 HCC xenografts derived from 11 HCC biopsies and 3 lymphoma xenografts derived from 3 HCC biopsies. RNA-sequencing was performed using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (lllumina). SR126 sequencing was performed on an Illumina HiSeq 2500 using v4 SBS chemistry according to the manufacturer’s guidelines.
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Project description:All 122 HCC biopsies and 115 non-tumoral tissues from 114 patients were subjected to whole-exome sequencing. Whole-exome capture was performed using the SureSelectXT Clinical Research Exome (Agilent Technologies) or SureSelect Human All Exon V6+COSMIC (Agilent Technologies) platforms according to the manufacturer’s guidelines. Sequencing was performed on an Illumina HiSeq 2500 at the Genomics Facility Basel according to the manufacturer’s guidelines. Paired-end 101-bp reads were generated.
| EGAD00001008182 | EGA
Project description:Bulk RNA-seq data of 8 RNA samples were generated. Libraries were prepared using the Stranded mRNA Library Prep, Ligation Kit (Illumina) following manufacturer’s recommendations and sequenced on a NextSeq 2000 (2x50 bp, Illumina).
| EGAD00001010308 | EGA
Project description:RNA-Seq procedure was used for analysis of expression in HEK293T cells. Cells were separately lysed with Trizol reagent (Invotrogen). Total RNA was extracted from cell lysed with Trizol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA quality was checked with BioAnalyser and RNA 6000 Nano Kit (Agilent). Poly(A)+ RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 10 millions of reads were generated for each sample.
2019-12-03 | GSE130262 | GEO
Project description:RNA-Seq procedure was used for analysis of expression in melanoma cells. Cells were separately lysed with Trizol reagent (Invotrogen). Total RNA was extracted from cell lysed with Trizol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA quality was checked with BioAnalyser and RNA 6000 Nano Kit (Agilent). Poly(A)+ RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 14.8 millions of reads were generated for each sample.
2024-05-10 | GSE221873 | GEO
Project description:RNA-Seq procedure was used for analysis of expression in melanoma cells. Cells were separately lysed with Trizol reagent (Invotrogen). Total RNA was extracted from cell lysed with Trizol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA quality was checked with BioAnalyser and RNA 6000 Nano Kit (Agilent). Poly(A)+ RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 14.8 millions of reads were generated for each sample.
2024-05-10 | GSE221872 | GEO
Project description:RNA-Seq procedure was used for analysis of expression in HEK293T cells. Heat shock treatments was performed for 20 min at 43°C. Then heat shock treated cells were incubated for 6 h at 37°C and replicates were separately lysed with Trisol reagent. Total RNA was extracted from cell lysed with Trisol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA Quality was checked with BioAnalyser and RNA 6000 Nano Kit(Agilent). Poly(A)+ RNA was isolated with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length.
2019-12-03 | GSE130493 | GEO
Project description:For analysis of mRNA expression levels, total RNA was harvested from each cell-line in replicate with Trizol™ (Thermo scientific). Total RNA was purified using Direct-zol™ columns according to the manufacturers specifications (Zymo Research). For cDNA synthesis 1 μg of total RNA was process as the T12VN-PAT assay (Jänicke et al., RNA 2012), except that this was adapted for multiplexing on the Illumina MiSeq instrument. We refer to this assay as mPAT for multiplexed PAT. The approach is based on a nested-PCR that sequentially incorporates the Illumina platform’s flow-cell specific terminal extensions onto 3’ RACE PCR amplicons. First, cDNA was generated using the anchor primer mPAT Reverse, next this primer and a pool of 50 gene-specific primers were used in 5 cycles of amplification. Each gene-specific primer had a universal 5’ extension (see supplementary file primers) for sequential addition of the 5’ (P5) Illumina elements. These amplicons were then purified using NucleoSpin columns (Macherey-Nagel), and entered into second round amplification using the universal Illumina Rd1 sequencing Primer and TruSeq indexed reverse primers from Illumina. Second round amplification was for 14 cycles. Note, that each experimental condition was amplified separately in the first round with identical primers. In the second round, a different indexing primer was used for each experimental condition. All PCR reactions were pooled and run using the MiSeq Reagent Kit v2 with 300 cycles (i.e. 300 bases of sequencing) according to the manufacturers specifications. Data were analysed using established bioinformatics pipelines (Harrison et al., RNA 2015)
2016-09-08 | GSE84913 | GEO
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:294 formalin-fixed paraffin-embedded (FFPE) tissue samples were sent to the UNC Lineberger Comprehensive Cancer Center Translational Genomics Lab (TGL) for RNA isolation using the Maxwell 16 MDx Instrument (Promega AS3000) and the Maxwell 16 LEV RNA FFPE Kit (Promega AS1260) following the manufacturer’s protocol (Promega 9FB167). 279 total RNA sequencing libraries were prepared at TGL using a Bravo Automated Liquid-Handling Platform (Agilent G5562A) and the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina 20020599) following the manufacturer’s protocol (Illumina 1000000040499). RNAseq library quality and quantity were measured using a TapeStation 4200 (Agilent G2991AA) and Qubit 3.0 fluorometer (Life Technologies Q33216), pooled at equal molar ratios, and denatured following the manufacturer’s protocol (Illumina 1000000106351). 271 total RNA sequencing libraries were sequenced at TGL on NovaSeq 6000 (Illumina 20012850) S4 flow cells (Illumina 20028313) following the manufacturer’s protocol (Illumina 1000000019358) using a 2x50 bp paired-end configuration and pool sizes of 91 libraries to target a read depth of 110 million clusters per library on average.
| EGAD00001010201 | EGA