A310386c-6f43-4a92-8d08-ee5d6e730956 - samples
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ABSTRACT:
PROVIDER: EGAD00001007644 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:This study mapped the genome wide DNA methylation changes in whole blood and buccal swab samples of 2 year old male rhesus monkeys subjected to parental deprivation in their first months of life (surrogate peer-reared condition). Equal numbers of control mother-reared (MR) and surrogate peer-reared (SPR) male monkeys whole blood (5 vs 5) and buccal swab samples (3 vs 3) were analyzed by methylated DNA immunoprecipitation (MeDIP) coupled with promoter tiling arrays.
2016-07-06 | E-GEOD-84020 | biostudies-arrayexpress
Project description:This study mapped the genome wide DNA methylation changes in whole blood and buccal swab samples of 2 year old male rhesus monkeys subjected to parental deprivation in their first months of life (surrogate peer-reared condition).
2016-07-06 | GSE84020 | GEO
Project description:Whole exome sequencing of 5 HCLc tumor-germline pairs. Genomic DNA from HCLc tumor cells and T-cells for germline was used. Whole exome enrichment was performed with either Agilent SureSelect (50Mb, samples S3G/T, S5G/T, S9G/T) or Roche Nimblegen (44.1Mb, samples S4G/T and S6G/T). The resulting exome libraries were sequenced on the Illumina HiSeq platform with paired-end 100bp reads to an average depth of 120-134x. Bam files were generated using NovoalignMPI (v3.0) to align the raw fastq files to the reference genome sequence (hg19) and picard tools (v1.34) to flag duplicate reads (optical or pcr), unmapped reads, reads mapping to more than one location, and reads failing vendor QC.
2016-02-01 | E-MTAB-4313 | biostudies-arrayexpress
Project description:These data corresponds to RNA-Seq assays obtained from the body wall of farmed I. badionotus juveniles samples. These raw reads were used to evaluate differential gene expression between wild and farmed Isostichopus badionotus specimens. With this aim, a de-novo transcriptome assembled from wild specimens was used as reference. Further information about de-novo assembled transcriptome is available within the BioProject PRJNA639785.
2020-09-01 | GSE157183 | GEO
Project description:To identify more targets in soybean, particularly specific targets of Cd-stress-responsive miRNAs, high-throughput degradome sequencing was used. In total, we obtained 8913111 raw reads from the library which was constructed from a mixture of four samples (HX3-CK, HX3-Cd-treatment, ZH24-CK and ZH24-Cd-treatment). After removing the reads without the CAGAG adaptor, 5430126 unique raw-reads were obtained. The unique sequences were aligned to the G. max genome database, and 6516276 reads were mapped to the genome. The mapped reads from the libraries represented 51481 annotated G. max genes.
2013-12-20 | GSE50063 | GEO
Project description:To understand the diversity of expression states within melanoma tumors, we obtained freshly resected samples, dissagregated the samples, sorted into single cells and profiled them by single-cell RNA-seq. Tumors were disaggregated, sorted into single cells, and profiled by Smart-seq2. *Raw data files absent for samples GSM1851356 and GSM1851494.* **Submitter declares reads will be made available through dbGaP.**
2016-04-05 | E-GEOD-72056 | biostudies-arrayexpress
Project description:Purpose: The goal of this study is to provided a comprehensive genomic information for functional genomic studies in Q. mongolica. Methods:The Quercus mongolica 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 52934562 raw reads were obtained from Illumina sequencing platform. After filtering out the low quality reads, we obtained 52076914 clean reads, which assembled into 39130 transcripts with a mean length of 742 bp and GC content of 42.12%, and 24196 unigenes with a mean length of 732 bp and GC content of 42.34%, based on Trinity assembly platform. Conclusions:RNA-Seq was applied to polyadenylate-enriched mRNAs from leaves of Q. mongolica 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 | GSE125799 | GEO
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
Project description:The affected twins have their lymph nodes and buccal swabs sequenced with WGS. The unaffected sibling have his/her buccal swab sequenced with WGS as control too.
| EGAD00001011118 | EGA
Project description:To characterize gene expression changes in AML induced by CNTRL-FGFR1, we used RNA-seq analysis of sorted Mac+Gr1+B220+ AML cells (n = 2) from the SP and BM of leukemic mice, as well as sorted Mac+Gr1+ myeloid cells (n=3) from normal mice. Methods: cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation kit following the manufacturer’s instructions. The quality of the resulting cDNA libraries were assessed using a Bioanalyzer DNA 1000 chip (Agilent) and quantified by quantitative PCR (Bio-Rad). The cDNA libraries were sequenced using paired end Illumina Hiseq2000 protocols (50 cycles). The Illumina sequencing pipeline version 1.8 was employed for transferring raw images to base calls, generating sequence reads, and de-multiplexing the reads. The generated FASTQ files were imported to CLC Genomics Workbench and aligned to the mouse genome, NCBI37/mm9. The transcript expression levels were determined in terms of number of reads per kilobase per million (RPKM) and compared between sorted normal myeloid (Gr1+Mac1+) cells and sorted leukemic myeloid cells. Results: The result showed a remarkable difference between normal (Gr1+Mac1+) and leukemic (Mac+Gr1+B220+) myeloid cells. Gene Set Enrichment Analysis and leading-edge analysis suggested that Mac+Gr1+B220+ cells have the potential to differentiate into either myeloid or T-cell, but not a B-cell, lineages. Quantitative RT-PCR analysis of lineage-specific genes showed increased expression of Flt3, Gfi1, and Kit related to early myeloid-lineage commitment, while genes related to myeloid differentiation, Irf8, Klf4, Csf1r, Myc, and Spi1 were decreased compared with normal myeloid cells. Quantitative RT-PCR also confirmed that the Cd3e and Lmo2 T-cell specific genes were markedly increased in AML cells. Conclusions: We demonstrate that the CNTRL-FGFR1 fusion kinase induces bi-lineage myeloid and T-lymphoid disease in model mice. Genetic and molecular analyses in these models demonstrated that multiple signaling pathways, specifically related to myeloid and T-lymphoid lineages, were altered in neoplasms, which underscores the importance of developing therapies that target all of these signaling pathways to eradicate the leukemia-initiating-cells RNA-seq analysis of sorted Mac+Gr1+B220+ AML cells (n = 2) from the SP and BM of leukemic mice, as well as sorted Mac+Gr1+ myeloid cells (n=3) from normal mice.
2013-06-20 | E-GEOD-48048 | biostudies-arrayexpress