Ena-DATASET-NCCS-29-09-2019-15:36:44:885-106 - samples
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ABSTRACT:
PROVIDER: EGAD00001005366 | EGA |
REPOSITORIES: EGA
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Project description:Whole-genome sequencing (WGS) was performed for 60 pairs of tumor-normal samples from patients diagnosed with NKTL. Genomic DNA from tumor tissue was extracted with QIAamp DNA Mini Kit. The DNA for the matching normal was obtained from blood or buccal swabs and purified by Blood and Cell Culture DNA Mini kit or E.Z.N.A. Tissue DNA Kit (Omega Bio-tek) according to manufacturer’s instructions. The quantity and quality were assessed by Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen) and agarose gel electrophoresis. All sequencing libraries were prepared using TruSeq Nano DNA Library Prep Kit (Illumina). Paired-end sequencing was performed on Illumina HiSeq 2000 or HiSeq X Ten as 2x101 bp or 2x151 bp, respectively.
| EGAD00001005231 | EGA
Project description:WGS and WTS data of a single patient diagnosed with HSTCL.
Whole-genome sequencing (WGS) was performed for the tumor-normal sample. Genomic DNA from tumor tissue was extracted with QIAamp DNA Mini Kit. The DNA for the matching normal was obtained from blood or buccal swabs and purified by Blood and Cell Culture DNA Mini kit or E.Z.N.A. Tissue DNA Kit (Omega Bio-tek) according to manufacturer’s instructions. The quantity and quality were assessed by Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen) and agarose gel electrophoresis. All sequencing libraries were prepared using TruSeq Nano DNA Library Prep Kit (Illumina). Paired-end sequencing was performed on Illumina HiSeq 4000 2x151 bp read length.
Whole-transcriptome sequencing (WTS): Total RNA from snap frozen EITL tumor samples was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. The integrity of RNA was determined by electrophoresis using 2100 Bioanalyzer (Agilent Technologies). 500 ng of total RNA was reverse transcribed with iScript cDNA Synthesis Kit (Bio-Rad, Hercules, CA, USA). Quantification was performed using SsoFast EvaGreen Supermix and CFX96 Real-Time PCR System (both Bio-Rad). Sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina) and WTS was performed on Illumina HiSeq 2500 with 2x101 bp read length.
| EGAD00001005229 | EGA
Project description:WGS from 4 patients, WTS from only 3 patients (insufficient tissue from 4th patient for WTS).
Whole-genome sequencing (WGS) was performed for 60 pairs of tumor-normal samples from patients diagnosed with NKTL. Genomic DNA from tumor tissue was extracted with QIAamp DNA Mini Kit. The DNA for the matching normal was obtained from blood or buccal swabs and purified by Blood and Cell Culture DNA Mini kit or E.Z.N.A. Tissue DNA Kit (Omega Bio-tek) according to manufacturer’s instructions. The quantity and quality were assessed by Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen) and agarose gel electrophoresis. All sequencing libraries were prepared using TruSeq Nano DNA Library Prep Kit (Illumina). Paired-end sequencing was performed on Illumina HiSeq 2000.
Whole-transcriptome sequencing (WTS): Total RNA from snap frozen EITL tumor samples was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. The integrity of RNA was determined by electrophoresis using 2100 Bioanalyzer (Agilent Technologies). 500 ng of total RNA was reverse transcribed with iScript cDNA Synthesis Kit (Bio-Rad, Hercules, CA, USA). Quantification was performed using SsoFast EvaGreen Supermix and CFX96 Real-Time PCR System (both Bio-Rad). Sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina) and WTS was performed on Illumina HiSeq 2500 with 2x101 bp read length.
Description of prefix used in filenames:
T: Tumor samples
N: Normal samples (Blood)
P: PDX samples
| EGAD00001005341 | EGA
Project description:Whole-genome sequencing (WGS) was performed for 13 pairs of tumor-normal samples from patients diagnosed with NKTL. Genomic DNA from tumor tissue was extracted with QIAamp DNA Mini Kit. The DNA for the matching normal was obtained from blood or buccal swabs and purified by Blood and Cell Culture DNA Mini kit or E.Z.N.A. Tissue DNA Kit (Omega Bio-tek) according to manufacturer’s instructions. The quantity and quality were assessed by Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen) and agarose gel electrophoresis. All sequencing libraries were prepared using TruSeq Nano DNA Library Prep Kit (Illumina). Paired-end sequencing was performed on Illumina HiSeq 2000 or HiSeq X Ten as 2x101 bp or 2x151 bp, respectively.
8 NKTL FFPE specimens were screened for somatic mutations using deep targeted capture sequencing (TCS). FFPE rolls or slides were extracted using QIAamp DNA FFPE Tissue kit (QIAGEN). The FFPE genomic DNA was treated with NEBNext FFPE DNA Repair Mix and assessed by Quant-it PicoGreen dsDNA Assay Kit (Invitrogen). The library was generated from 10-200 ng DNA with SureSelectXT Low Input Target Enrichment System for Illumina Paired-End Sequencing Library (Agilent Technologies) according to manufacturer’s instructions. RNA based probe was designed with SureDesign (Agilent Technologies) to target-capture 140 genes. Next, the captured libraries were pooled in equimolar concentration and sequenced on Illumina Novaseq 6000 platform with SP or S1 chip. Reads aligning to 40 selected genes were isolated post-alignment for this submission.
Prefix used in filenames:
T - Tumor samples
N - Matched-Normal samples
| EGAD00001004140 | EGA
Project description:Nannochloropsis gaditana cells were cultivated under continuous light as a control condition versus 3 different flashing light conditions (FL5, FL50 and FL500). This study is complementary to Lima et al. (2020) where physiology and photosynthetic capacity were assesed. Here we analyzed the mRNA expression level of key genes related to photoshynthesis, lipid and starch synthesis, and nitrogen assimilation. Total cell RNA was extracted from cultures of N. gaditana at a concentration of 1x106 cells/mL using the E.Z.N.A® total DNA/RNA isolation kit (Omega Bio-tek, Inc., USA). Reverse transcription reactions were performed using SuperScript™ IV VILO™ Master Mix with the enzyme ezDNase (Invitrogen™, ThermoFisher scientific, USA) according to the manufacturer’s protocol. The qPCR reactions were performed by mixing 5L of FastStart Universal SYBR Green Master mix (Rox) (Roche Molecular Systems, Inc., USA) with 1 L of primer mix (consisting of forward and the reverse primers) at a concentration of 300 nM and 4 L of the cDNA. The conditions of thermocycling were: 95 C for 600 s (preincubation), followed by 40 cycles of denaturation at 95 C for 10 s, annealing/extension at 60 C for 30 s. qPCR were performed in the LightCycler 96 Roche Life Science instrument.
2022-08-02 | GSE210188 | GEO
Project description:InvF, an AraC-type transcriptional activator, regulated the expression of genes that encoded the secreted effector molecules SipABCD, SigD, SptP, and SopE in Salmonella typhimurium. However, it seems that almost all effector homologs were lost in P. fluorescens 2P24. To identify the InvF regulon in strain 2P24, the invF deficient mutant 2P24ΔinvF was constructed, and we implemented transcriptome sequencing (RNA-seq). Both of strains 2P24 and 2P24ΔinvF were incubated in mannitol-glutamate (MG) minimal medium at 28℃ for 6 h and 12 h. The cell fractions were separated by centrifugation at 10, 000 rpm for 5 min at 4°C. Total RNA was isolated using a E.Z.N.A.® Bacterial RNA Kit (Omega Bio‐tek, USA) as described by the manufacturer for RNA-seq. mRNA profiles of strains 2P24 and 2P24ΔinvF were generated by deep sequencing, in triplicate, using Illumina Hiseq. A total of 127 significantly differentially expressed genes (DEGs) were obtained by comparing the transcriptional level of strain 2P24ΔinvF with 2P24 at 6 h and 12 h [Fold change ≥ 1.5; p value ≤ 0.05]. Fifty-two down-regulated genes were regarded as InvF regulon candidates. Among the InvF regulon candidates, 39 genes were screened based on their gene functional annotation for qRT-PCR verification. Finally, eight genes were confirmed to be regulated positively by InvF. They encoded dihydrolipoyl dehydrogenase, toxin-activating lysine-acyltransferase, phage infection protein, AsnC family protein, two hypothetical proteins, NAD(P)H dehydrogenase, and protein IolH, respectively.
2021-08-03 | GSE181272 | GEO
Project description:Purpose: The goals of this study are to compare CD115- monocytes to CD115+ monocytes from naïve and tumor-bearing mice (EL4) with high-throughput data analysis. Methods: CD115- monocytes and CD115+ monocytes were sorted by flow cytomentry separatly. Total RNA was extracted from cells using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) and residual DNA was removed with a DNA-free Kit (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s instructions. Samples were loaded onto a 1% agarose gel before electrophoresis. DNA-free conditions were confirmed by SYBR Gold staining (Invitrogen). The quantity and the quality of RNA was evaluated by Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific) and bioanalyzer (Agilent 2100; Agilent Technologies, Santa Clara, CA, USA). RNA-Seq libraries were prepared with 1 μg of total RNA from two biological replicates of each group using TruSeq Stranded mRNA LT Sample Prep Kit and analyzed by Illumina Sequencer (both from Illumina, San Diego, CA, USA). Results: We found 1,723 differetially expressed genes (DEGs) between CD115- monocytes and CD115+ monocytes (cutoff value was set at 2-fold). DEGs of interest are invoved in granulocyte, transcription factors, mononuclear phagocytes, and angiogenesis. Conclusions: Our study represents the first detailed DEGs analysis of CD115- monocytes and CD115+ monocytes from naïve and tumor-bearing mice. Our results show that CD115- monocytes may have a closer relationship with neutrophils or PMN-MDSCs than the CD115+ monocytes. Also, our overall transcriptomic analysis further suggests that CD115- M-MDSCs and monocytes are separate subsets of monocytic cells.
2022-03-22 | GSE199008 | GEO
Project description:Human plasma (from both healthy donors and disease) were isolated as described using Norgen plasma/serum exosome purification mini kit, and albumin depleted (HSA depletion kit, Thermo Fisher). Here we show that psEV (plasma small extracellular vesicles) are distinct in their proteome, psEV are biologically active, reflecting cell migratory capacity
2021-03-18 | PXD021856 | Pride
Project description:Genomic DNA of intracranial aneurysm and matched superficial temporal artery from same patient (n=9) was extracted with QIAamp DNA Mini Kit (Qiagen, Valencia, CA). A total of 500 of genomic DNA was bisulfite conversion using the EZ DNA Methylation Gold Kit (Zymo Research, Irvine, CA) and then analyzed on an Infinium HumanMethylation450 BeadChip (Illumina, San Diego, CA) following the manufacturer’s instructions.
2016-12-01 | GSE75434 | GEO
Project description:RNA from sciatic nerves was isolated from HSF WT and HSF V30M mice with RNeasy Mini columns and first-strand complementary DNA (cDNA) was synthesized using the SuperScript double-stranded cDNA Kit.
2021-01-20 | GSE165126 | GEO