Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ena-DATASET-GIS-27-11-2017-03:29:14:222-144 - samples

ABSTRACT: The dataset includes a subset of 762 individuals that were found to be closely related (≤3rd degree), including 263 Chinese and 499 Malays from the Singapore Living Biobank. There samples are whole-exome sequenced on Illumina HiSeq2000 platform (125bp paired end) with the exonic regions being captured using the Nimblegen SeqCap EZ Exome v3 kits.All the files are in the BAM format.

PROVIDER: EGAD00001003819 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Antiviral and anti-inflammatory properties of novel anti-HIV candidate ABX464 promotes specifics RNA splicing while preserving cellular RNA integrity.

Project description:Purpose: To ensure that ABX464 acted specifically on HIV splicing and did not significantly or globally affect the splicing events of human genes, we used an assembly approach of HIV (YU2 strain) putative transcripts and human long non-coding sequences from paired-reads (2x75bp) captured on a NimbleGen SeqCap® EZ Developer Library (Roche/NimbleGen). Methods: Cells were infected with 80 ng of p24/106 cells of the YU-2 strain for 4 to 6 hours and then rinsed with PBS before medium renewal, followed by high-throughput RNAseq from custom SeqCap EZ capture libraries. Each raw dataset of the samples contained between 5 and 30 million paired-end reads (75 bp), with an average of approximately 12 million raw reads per sample. Results: The raw reads were then cleaned and assembled per library to generate contigs, giving an average of 930 contigs per sample for further analyses. Conclusions: Our results show that high-throughput analyses coupled with bioinformatics-specific tools offers a comprehensive and more accurate view of mRNA splicing within a cell.

2018-12-31 | GSE120109 | GEO

DNA sequencing comparing different stages of leukemic progression in a mouse model of severe congenital neutropenia (SCN)

Project description:To address how Csf3r and RUNX1 mutations in combination with CSF3 administration affect hematopoiesis in vivo, we performed serial transplantation experiments. Lineage-negative Csfr-d715 BM cell cells were lentivirally transduced with the patient specific RUNX1-D171N (RHD) mutant or an empty vector control. Primary recipients showed a pre-leukemic condition characterised by myeloblasts in the peripheral blood, but not overt AML. Upon serial transplantation, one of the Csfr-d715/RUNX1-D171N mutant mice, treated with CSF3, could repopulate secondary and tertiary recipients. Whole exome sequencing on these mice were performed to investigate whether these mice acquired an additional mutation. Enzymatically fragmented genomic DNA was used to construct sample libraries following the SeqCap EZ HyperPlusCap workflow User’s Guide version 1.0 (Roche). Unique, dual index adapters (Integrated DNA technologies) were used for ligation. After ligation of adapters and an amplification step, exome target sequences were captured using in-solution oligonucleotide baits (SeqCap EZ Developer Library mm9_exome_L2R_D02). Amplified captured sample libraries were paired-end sequenced on the HiSeq 2500 platform (Illumina).

2020-08-24 | E-MTAB-9376 | biostudies-arrayexpress

ena-DATASET-sacgf-28-09-2019-00:47:29:060-90 - samples

Project description:Exome sequencing data of two siblings of with a neurodegenerative phenotype due to SMVT deficiency. Exonic sequences were enriched using the SeqCap EZ Human Exome Library v3.0 kit (Roche NimbleGen) and libraries sequenced as 100bp paired-end reads on the HiSeq 2000 platform (Illumina).

| EGAD00001005364 | EGA

Project description:The Singapore Living Biobank is a collection of healthy population-based Chinese and Malay individuals, for the purpose of phenotype recall study of high-impact variant carriers. These individuals are sampled from two studies: Multi-Ethnic Cohort (MEC), and the Singapore Health 2012 (SH2012). The MEC is a population-based cohort initiated in 2007 to investigate the genetic and lifestyle factors that affect the risk of developing chronic diseases such as diabetes and cardiovascular outcomes in the three ethnic groups (Chinese, Malays, and Indians). The SH2012 study is a population-based cross-sectional survey conducted in Singapore between 2012 and 2013, with over-sampling of Malays and Indians. Participants in MEC and SH2012 completed a similar set of questionnaire components, health examination, and biochemisty panels. Description of the MEC and SH2012 studies can be found at http://blog.nus.edu.sg/sphs/. We generated whole-exome sequencing data and Illumina OmniExpress array genotyping data for 1,299 Chinese and 1,229 Malays from the Singapore Living Biobank. This study includes a subset of 762 individuals that were found to be closely related (≤3rd degree), including 263 Chinese and 499 Malays.

| EGAS00001002619 | EGA

EGAS00001001194-sept_2011 - samples

Project description:TwinsUK whole exome sequencing using NimbleGen SeqCap EZ

| EGAD00001001382 | EGA

Expression data of ECa9706 over expressing miR-144/451 cluster

Project description:miR-144/451 cluster is highly conversed in different species, miRbase database shows miR-144/451 cluster is constituted by miR-144-3p, miR-144-5p, miR-451a. Low-expression of miR-144/451 was closely related with the risk for esophageal cancer We used microarrays to identify the differentially expressed genes in ECa9706 over expressing miR-144/451 cluster

2018-08-08 | GSE118249 | GEO

ffe007b3-c102-4716-85e9-c13ef839a867 - samples

Project description:Bam file from exome sequencing of FFPE sample from Ly3 using SeqCap EZ Human Exome Library (Roche Nimblegen, Inc., WI, USA) and Illumina HiSeq2000 sequencer.

| EGAD00001004782 | EGA

J_Costello_20170925_dataset_1 - samples

Project description:15 whole exome sequencing datasets from five patients. Data is provided as bam files. Libraries were generated using the SeqCap EZ Exome v3.0 kit and sequenced on an Illumina sequencer

| EGAD00001003763 | EGA

222

Project description:222

| PRJEB34284 | ENA

Project description:SeqCap Epi Target Capture of Pancreatic Cancer

| PRJNA672914 | ENA