885a0fd1-595e-479d-bed5-dfc88e5d40ae - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001009169 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:The Columbia Alzheimer’s dataset (white matter) consists of 24 white matter individuals (12 controls, 12 cases). A total of 12,000 estimated cells from each sample were loaded on the 10x Single Cell Next GEM G Chip. cDNA libraries were prepared using the Chromium Single Cell 3’ Library and Gel Bead v3 kit according to the manufacturer’s instructions. cDNA libraries were sequenced using the Illumina NovaSeq 6000 System and NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles), aiming at a sequencing depth of minimum 30K reads/nucleus.
| EGAD00001009168 | EGA
Project description:The Roche Alzheimer’s disease dataset (Roche_AD) consists of 80 samples from 40 unique individuals (one sample from the temporal cortex and one from deep white matter for each individual, 12 cases, 25 controls, 3 dementia). A total of 12,000 estimated cells from each sample were loaded on the 10x Single Cell Next GEM G Chip. cDNA libraries were prepared using the Chromium Single Cell 3’ Library and Gel Bead v3 kit according to the manufacturer’s instructions. cDNA libraries were sequenced using the Illumina NovaSeq 6000 System and NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles), aiming at a sequencing depth of minimum 30K reads/nucleus.
| EGAD00001009166 | EGA
Project description:The goal of this study is to identify novel target genes of DVL3 in two breast cancer cell lines Methods:Total RNA was isolated using the Aurum™ Total RNA Mini Kit (Bio Rad) and library preparation and sequencing were performed at Center for Biotechnology & Genomics of Texas Tech University. RNA quality was determined using RNA Screen Tape (Agilent). Ribosomal RNA depletion was achieved using NEB Next rRNA Depletion Kit (Human/Mouse/Rat) (NEB # E6310X). RNA fragmentation, double stranded cDNA and adaptor ligation was generated using NEBNext Ultra II Directional RNA Library Prep according to the manufacturer’s protocol (NEB # E7760L). PCR enriched libraries were quantified by Qubit and equimolar indexed libraries (different samples had different indexes for multiplexing) were pooled. Pooled libraries were quantitatively checked using the Agilent Tapestation 2200 and quantified using Qubit. The libraries were then diluted to 200 pM and spiked with 2% phiX libraries (Illumina control). The transcriptome sequencing was performed on the barcoded stranded RNA-Seq libraries using Illumina NovaSeq 6000 SP flow cell, paired-end reads (2 × 50 bp).
2021-04-16 | GSE165773 | GEO
Project description:Human PCNSL tumor samples were obtained surgically from clinical patients confirmed by pathology from our hospital. After sample collection processing and suspensions, we performed scRNA-seq following the manufacturer’s protocol. Briefly, the cells were washed with PBS and resuspended in 500 μl PBS. scRNA-seq libraries were prepared using a Chromium Single cell 3’ Reagent kit, version 2. Amplified cDNA and final libraries were evaluated using a High Sensitivity DNA Kit (Agilent Technologies). Sequencing was performed on NovaSeq 6000 (Illumina) at a depth of approximately 400M reads.
2021-09-23 | GSE181304 | GEO
Project description:To address how CSF3R mutations affect hematopoiesis in a severe congenital neutropenia (SCN) background we used SCN patient, or control, derived induced pluripotent stem cells (iPSC). HPCs were generated from CRISPR-Cas9 genome edited CSF3R-d715 SCN or control-derived iPSCs with the STEMdiff™ Hematopoietic Kit (STEMCELL Technologies). Floating cells were harvested at Day 12 of the hematopoietic induction protocol. CD34+CD45+ HPCs were FACS sorted in TRIzol and RNA was isolated according to the manufacturer’s protocol. SMARTer Ultra Low Input RNA kit for sequencing (Clontech, v4 Cat# 634891) was used to generate cDNA. Sequencing libraries were generated using TruSeq Nano DNA Sample Preparation kits (Illumina, Cat# 20015964), according to the low sample protocol and paired-end sequenced on a HiSeq 2500 or Novaseq 6000 (both Illumina).
2021-04-01 | E-MTAB-10288 | biostudies-arrayexpress
Project description:10X Genomics scRNA- and TCR-sequencing (Chromium Next GEM Single Cell 5’
Reagent Kit v1.1) was performed on the plasma cell depleted mononuclear
fraction of bone marrow aspirates from 6 patients with newly diagnosed
multiple myeloma. Generated gene expression libraries were paired-end sequenced on the NovaSeq
6000 S2. Generated V(D)J libraries were paired-end sequenced on the NextSeq
550.
| EGAD00001009270 | EGA
Project description:Purpose : The goal of this study was to use RNA Seq to explore the correlation of gene expression of a collection of clinical P. aeruginosa isolates to various phenotypes, such as colony morphology, c-di-GMP production and biofilm formation Methods : mRNA profiles were generated for Pseudomonas aerugionsa clinical samples by deep sequencing.Ribosomal RNA was removed by using the RiboZero Bacteria kit (Illumina). cDNA libraries were synthesized using the SMARTScribe Reverse Transcriptase (Takara) followed by a PCR enrichment using the AccuPrime HiFi Taq polymerase (Invitrogen). Enzymatic reactions were carried out in the presence of SUPERase·In™ RNase Inhibitor (Invitrogen); RNACleanXP beads (Agencourt) were used for all RNA purification steps. Quality checks were performed before, during and after cDNA library preparation with the RNA Nano Kit and an Agilent Bioanalyzer 2100 (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq 6000 (paired-end mode; 2 x 50 bp) and mRNA reads were trimmed using the tool ‘cutadapt’ (version 3.5) with customized settings and mapped to the NC_008463.1 (PA14) reference genome from NCBI using ‘bowtie2’ (version 2.3.5.1) with the settings “--very-sensitive-local; --no-mixed; --fr; --no-unal”.
2022-11-05 | GSE147921 | GEO
Project description:Purpose : The goal of this study was to use RNA Seq to explore the success of lasR mutants in the opportunistic pathogen Pseudomonas aeruginosa in a clinical context by profiling the functional consequences of patho-adaptive mutations in clinical isolates. Methods : mRNA profiles were generated for Pseudomonas aerugionsa samples by deep sequencing.Ribosomal RNA was removed by using the RiboZero Bacteria kit (Illumina). cDNA libraries were synthesized using the SMARTScribe Reverse Transcriptase (Takara) followed by a PCR enrichment using the AccuPrime HiFi Taq polymerase (Invitrogen). Enzymatic reactions were carried out in the presence of SUPERase·In™ RNase Inhibitor (Invitrogen); RNACleanXP beads (Agencourt) were used for all RNA purification steps. Quality checks were performed before, during and after cDNA library preparation with the RNA Nano Kit and an Agilent Bioanalyzer 2100 (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq 6000 (paired-end mode; 2 x 50 bp) and mRNA reads were trimmed using the tool ‘cutadapt’ (version 3.5) with customized settings and mapped to the NC_008463.1 (PA14) reference genome from NCBI using ‘bowtie2’ (version 2.3.5.1) with the settings “--very-sensitive-local; --no-mixed; --fr; --no-unal”.
2022-02-23 | GSE191103 | GEO
Project description:To address how CSF3R and RUNX1 mutations affect hematopoiesis in a severe congenital neutropenia (SCN) background we used SCN patient, or control, derived induced pluripotent stem cells (iPSC). HPCs were generated from CRISPR-Cas9 genome edited CSF3R-d715 SCN or control-derived iPSCs with the STEMdiff™ Hematopoietic Kit (STEMCELL Technologies). The RUNX1-D171N (RHD) mutation, or an empty vector control, was lentivirally introduced to the hematopoietic induction cultures 60 hours before harvesting the floating cells. Floating cells were harvested at Day 12 of the hematopoietic induction protocol. CD34+CD45+ HPCs were FACS sorted in TRIzol and RNA was isolated according to the manufacturer’s protocol. SMARTer Ultra Low Input RNA kit for sequencing (Clontech, v4 Cat# 634891) was used to generate cDNA. Sequencing libraries were generated using TruSeq Nano DNA Sample Preparation kits (Illumina, Cat# 20015964), according to the low sample protocol and paired-end sequenced on a HiSeq 2500 or Novaseq 6000 (both Illumina).
2020-08-24 | E-MTAB-9375 | biostudies-arrayexpress
Project description:Purpose: We investigated the function of overexpressed BCL2L14-ETV6 fusion variants in triple-negative breast cancer using high-throughput mRNA sequencing (RNA-Seq) analysis in BT20 human basal-like breast cancer cell line. Methods: The BCL2L14-ETV6 fusion variants or wildtype ETV6 cDNA containing the full-length ORFs were subcloned into the lentiviral pLenti7.3 vector, and later transduced into the BT20 cell line. BT20 cells were cultured in EMEM (ATCC) with 10 % fetal bovine serum (Hyclone). Total RNA was extracted from cells in individual confluent 10 cm dish, using the standard procedure of Qiagen RNeasy kit. The NovaSeq 6000 library for DNA sequencing was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following the protocol provided by the manufacturer. The final libraries were normalized by quantification with LightCycler 480 II (Roche Applied Science, Indianapolis, IN, USA) and qualification with Bioanalyzer (Agilent, Palo Alto, CA, USA). The final loading concentration was adjusted to 10 pM following the NovaSeq 6000 loading protocol. The NovaSeq 6000 S2 Reagent Kit (Illumina) was used for paired-end reads (2×150 bp) sequencing reactions. Sequencing data was given as raw data with a Phred Q30 score of 80 or better. Results: Confirming the overexpression of BCL2L14-ETV6 fusion variants, the reads that match to partial of BCL2L14 and ETV6 mRNA transcripts were 32~256 fold higher in the stable BT20 cell lines expressing BCL2L14-ETV6 fusion, compared to the cells the express the vector control. We found some key genes in cell migration and invasion are up-regulated in these stable BT20 cells compared with the cells the express the vector control and the wildtype ETV6. Conclusions: BCL2L14-ETV6 fusions endow enhanced cell migration and invasion in breast cancer.
2020-03-28 | GSE120919 | GEO