|
| Status |
Public on Jan 09, 2016 |
| Title |
500_cell_ATAC-seq_with_Tn5059_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
GM12878 B-Lymphocytes
|
| Organism |
Homo sapiens |
| Characteristics |
passage: P10-20
ethnicity: Caucasian
Sex: female
cell line: GM12878
|
| Growth protocol |
GM12878 cells were maintained in RPMI 1640. Cells were kept in suspension at 37°C and were harvested when suspensions reached optimal density.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
GM12878 cells were pelleted at 250 x g, and washed twice then resuspended in PBS before being used for the assay
ATAC-seq with optimized buffer and protease treatment after tagmentation was performed on lysed cells, followed by PCR cycling until curves reach saturation, and after gel size selection libraries are ready for sequencing. THS-seq method used a custom transposon and engineered Tn5 for tagging accessible regions, followed by in vitro transcription. RNA processing consisted of: MMLV first strand synthesis, RNase H digestion, second strand synthesis with Taq polymerase, custom transposon mediated fragmentation, and PCR barcode addition. Then libraries are ready for sequencing.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ATAC-seq
downsampled.bed: data downsampled to 8,351,125 reads for analysis
|
| Data processing |
Basecalls performed using Real Time Analysis (RTA) version 1.13
After demultiplexing sequences were aligned to the hg19 genome assembly using default BWA parameters
If needed samples were downsampled to the same number of unique reads with in house scripts before analysis
Peak calling was performed with Dfilter 1.0 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: .bed files of called peaks from Dfilter, with chromosomal locations of each significnatly called peak
|
| |
|
| Submission date |
Aug 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kun Zhang |
| E-mail(s) |
kzhang@eng.ucsd.edu
|
| Phone |
8585341348
|
| Organization name |
University of California San Diego
|
| Department |
Bioengineering
|
| Street address |
9500 Gilman Drive, MC0412, PFBH402
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE72089 |
Validation of THS-seq method, and comparison of published ENCODE DNase-seq data, self-generated ATAC-seq data and published ATAC-seq data, and THS-seq data for quantitation of chromatin accessibility. |
|
| Relations |
| BioSample |
SAMN03998277 |
| SRA |
SRX1156453 |
