Ontology highlight
ABSTRACT:
PROVIDER: PRJEB18921 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1780838.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 1 of 1 |
Similar Datasets
Project description:Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing - DS3
| PRJEB18922 | ENA
Project description:Contaminated aquifer (Dusseldorf-Flinger, Germany) templates extracted from 5 sediment depths ranging between 6.4 and 8.4 m below ground and over 3 years of sampling were amplified for amplicon pyrosequencing using the primers Ba27f (5’-aga gtt tga tcm tgg ctc ag-3’) and Ba519r (5’- tat tac cgc ggc kgc tg-3’), extended as amplicon fusion primers with respective primer A or B adapters, key sequence and multiplex identifiers (MID) as recommended by 454/Roche. Amplicons were purified and pooled as specified by the manufacturer. Emulsion PCR (emPCR), purification of DNA-enriched beads and sequencing run were performed following protocols and using a 2nd generation pyrosequencer (454 GS FLX Titanium, Roche) as recommended by the developer. Quality filtering of the pyrosequencing reads was performed using the automatic amplicon pipeline of the GS Run Processor (Roche), with a slight modification concerning the valley filter (vfScanAllFlows false instead of TiOnly) to extract the sequences. Demultiplexed raw reads were furhter trimmed for quality and lenght (>250 bp).
2012-11-11 | GSE25345 | GEO
Project description:Amplicon-based targeted re-sequencing analysis was performed in the patient-derived gliobastoma cell culture samples. For this purpose, genomic DNA (gDNA) was isolated and DNA libraries were prepared using the TruSeq Custom Amplicon Low Input (Illumina, Inc.) technology. By this, a pool of 375 amplicons was generated for each single sample in order to enrich for the target genes ATRX1, EGFR, IDH1, NF1, PDGFRA, PIK3CG, PIK3R1, PTEN, RB1 and TP53. Sequencing was performed on the Illumina MiSeq® next generation sequencing system (Illumina Inc.) and its 2 x 250 bp paired-end v2 read chemistry. The resulting reads were quality controlled and mapped against the human reference genome (hg19). For all samples, sequence variations of the amplified regions of interest in comparison to the human reference sequence were identified and filtered based on reliability.
2021-07-07 | E-MTAB-9343 | biostudies-arrayexpress
Project description:Genome editing was conducted on a t(3;8) K562 model to investigate the effects of deleting different modules or CTCF binding sites within the MYC super-enhancer. To check mutations after targeting with CRISPR-Cas9 we performed amplicon sequencing using the Illumina PCR-based custom amplicon sequencing method using the TruSeq Custom Amplicon index kit (Illumina). The first PCR was performed using Q5 polymerase (NEB), the second nested PCR with KAPA HiFi HotStart Ready mix (Roche). Samples were sequenced paired-end (2x 250bp) on a MiSeq (Illumina).
2021-07-26 | E-MTAB-9937 | biostudies-arrayexpress
Project description:Purpose: The goal of this study is to screen the candidate genes involved in drought avoidance of Q. liaotungensis Methods:The Q. liaotungensis leaves were generated by deep sequencing, using Illumina Hiseq 4000. The high-quality reads were obtained by removing the reads that contained adaptor contamination, low quality bases and undetermined bases.The transcriptome were de novo assembly. Results:A total of 54153182 raw reads were obtained from Illumina sequencing platform, and 53021436 clean reads were generated after filtering out the low quality reads. The clean reads were assembled into 41207 transcripts with median length 704 and GC content 42.17%, and 25593 unigenes with median length 687 and GC content 42.31%, based on Trinity assembly platform Conclusions:RNA-Seq was applied to polyadenylate-enriched mRNAs from leaves of Q. liaotungensis to obtain the transcriptome. De novo assembly was then applied followed by gene annotation and functional classification. The SSRs and SNPs were also obtained using assembled transcripts as reference sequences. The results of this study lay the foundation for further research on genetic diversity of Quercus.
2019-01-29 | GSE125798 | GEO