|
| Status |
Public on Jan 09, 2018 |
| Title |
WT bulkm [exome] |
| Sample type |
SRA |
| |
|
| Source name |
K562 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
tissue: Bone Marrow
genotype: wild type
|
| Growth protocol |
All cell lines were cultured in IMDM medium supplemented with 10% fetal bovine serum and antibiotics and were incubated at 37°C in a humidified atmosphere of 95% air and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole-exome sequencing of extracted DNA was performed to confirm DNMT3A mutations. Library construction, exon capture, and sequencing was performed by Otogenetics (Atlanta, GA, USA).
In brief, paired-end libraries were generated using the Illumina TruSeq DNA sample preparation kit. Exons were enriched using the Agilent Human All Exon V5 (51 Mb) capture system. Illumina HiSeq2500 was used for sequencing with a paired-end sequencing length of 100-125 bp and approximately 70 million reads per sample.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: Exome-seq
The data sets have been analyzed with BWA mapping + GATK SNP/Indel pipeline followed by snpEff annotation against reference genome hg19.
Then BAM files were analyzed for DNMT3A mutations
Genome_build: hg19
Supplementary_files_format_and_content: excel file for variants called (VCF)
|
| |
|
| Submission date |
Mar 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Valentina Giudice |
| E-mail(s) |
[email protected]
|
| Organization name |
NHLBI
|
| Department |
Hematology Branch
|
| Street address |
10 Center Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20814 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE96625 |
Abnormal RNA splicing and genomic instability after induction of DNMT3A mutations by CRISPR/Cas9 gene editing [Exome-Seq] |
| GSE96635 |
Abnormal RNA splicing and genomic instability after induction of DNMT3A mutations by CRISPR/Cas9 gene editing |
|
| Relations |
| BioSample |
SAMN06603793 |
| SRA |
SRX2642003 |
