|
| Status |
Public on Aug 03, 2016 |
| Title |
Control_KD_input_DNA |
| Sample type |
SRA |
| |
|
| Source name |
A549 cells_input_control_KD
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
knockdown: control KD
|
| Treatment protocol |
For RNAi, cells were transfected twice, 24 h apart, using 40 nM siRNA (final concentration) and Lipofectamine 2000 (Invitrogen). G1/S synchronized cells were obtained by double thymidine block procedure; cells were cultured for 16 hours in the presence of 2 mM thymidine, 9 hours in normal medium and then again 16 hours in the presence of 2 mM thymidine.
|
| Growth protocol |
A549 cells were cultured in RPMI 1640 medium supplemented with 10% fetal calf serum. Cells were maintained at 37°C in the presence of 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For the ChIP, cells were cross-linked with 1% formaldehyde and chromatin prepared by sonication to obtain DNA fragments between 100 bp and 500 bp. DDX11 bound DNA was then immunoprecipitated using the anti-DDX11 antibody (ab66971, Abcam), decrosslinked and extracted for analysis by sequencing
Libraries were prepared using the NEBNext Ultra DNA Library Prep Kit (Illumina)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were generated using bedtools v2.17.0
|
| |
|
| Submission date |
May 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Maite Huarte |
| E-mail(s) |
[email protected]
|
| Organization name |
CIMA
|
| Street address |
c/ Avd Pio XII, 55
|
| City |
Pamplona |
| State/province |
Navarra |
| ZIP/Postal code |
31008 |
| Country |
Spain |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE81600 |
A long noncoding RNA regulates sister chromatid cohesion [ChIP-seq] |
| GSE81602 |
A long noncoding RNA regulates sister chromatid cohesion |
|
| Relations |
| BioSample |
SAMN05011963 |
| SRA |
SRX1772383 |
