|
| Status |
Public on Jul 19, 2015 |
| Title |
Na_PDS_1 |
| Sample type |
SRA |
| |
|
| Source name |
DNA purchased from Coriell Institute for Medical Research
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: NA18507
sample type: Read-1: Na+ sequencing; Read-2: PDS+Na+ sequencing
|
| Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA18507
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
not applicable, DNA purchased from Coriell Institute for Medical Research
Illumina TruSeq DNA sample prep kit was used to prepare all samples
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
library strategy: G4-seq
|
| Data processing |
Fastq files (Read-1) containing 150 bp single-end reads were aligned to the humang genome (hg19) using bwa mem. Read-2 files were assigned to the same genomic location of the corresponding Read-1 files.
Bam alignment files were converted to bed files and processed with bedtools: 1) bamToBed conersion; 2) bed file expansion (slopBed -s -r 30); 3) grouping to keep only best alignments (groupBy -g 4 -c 5 -o max); 4) fasta sequence extraction (bedtools getfasta -s)
fasta sequence files and original fastq file were processed in R to compare Read-1 to Read-2 files: sequence tails beyond poly-A (>9) were trimmed; difference in quality score and base mismatches was calculated for each pair of reads; single-base mismatch values were averaged for all reads overlapping each aligned genomic location.
Genome_build: hg19
|
| |
|
| Submission date |
Dec 04, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Giovanni Marsico |
| E-mail(s) |
persego@gmail.com
|
| Organization name |
CRUK Cambridge Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE63874 |
High-throughput sequencing of DNA G-quadruplex structures in the human genome |
|
| Relations |
| BioSample |
SAMN03253033 |
| SRA |
SRX796470 |
