|
| Status |
Public on Jul 26, 2013 |
| Title |
K562 input |
| Sample type |
SRA |
| |
|
| Source name |
K562_TALE-3XFlag_input
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
cell type: erythrocytic leukaemia cells
transfected with: 20ug TALE:3X Flag Plasmid
chip antibody: none
|
| Treatment protocol |
For transfection, 5 X 10^6 cells per transfection were washed once with PBS.Cells were then transfected with 20 ug of TALE plasmid DNA or control mCherry plasmid by nucleofection with Lonza Kit V, as described by the manufacturer (Program T-016). Cells were immediately resuspended in K562 media at a cell density of 0.25 X 10^6 cells/ml.
|
| Growth protocol |
K562 erythrocytic leukaemia cells (ATCC CCL-243) were grown according to standard protocols in RPMI 1640 media (Invitrogen, 22400105) supplemented with 10% fetal bovine serum (FBS, Atlas Biologicals, F-0500-A) and 10% Penicillin/Streptomycin (Invitrogen, 15140122)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested at 72 hours for Sonication (flag) and ChIP
Library construction protocol: Single read - Illumina
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Sample 1
|
| Data processing |
imaging and basecalls from MiSeq RTA
Fastq files were aligned to hg19 using Bowtie
Duplicate reads were removed from BAM files using BAM tools
BAM was converted to WIG files using IGVtools
Genome_build: hg19
Supplementary_files_format_and_content: wig files generated using IGVtools
|
| |
|
| Submission date |
Jul 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Eric Mendenhall |
| Organization name |
Broad Institute
|
| Street address |
7 CC
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN02251027 |
| SRA |
SRX322538 |
| Named Annotation |
GSM1186138_K562_input.wig.gz |
