|
| Status |
Public on May 08, 2024 |
| Title |
ChIP_GFP+ control |
| Sample type |
SRA |
| |
|
| Source name |
Fetal Kidney
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: GFP_knockin
plasmid transfected: TET induced
cell line: Flp-In T-REx 293
|
| Treatment protocol |
Conditions used: HMGN5-FlpIn cell line induced for 24h with (1µg/µl Doxycycline); uninduced HMGN5-FlpIn cells as background, and GFP-FlpIn control cell line. (70% confluent 10cm culture dish per replicate)
|
| Growth protocol |
HMGN5-FlpIn cell lines were cultured in low glucose DMEM GlutaMAX™ supplemented with 10% Tetracycline-Free FBS (Biochrom), 100 µg/ml Hygromycin and 10 μg/ml Blasticidin, at 37°C and 5% CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated phenol/chloroform extraction
ChiP-Seq libraries were prepared using NEBNext® ChIP-Seq Library kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
Raw sequencing reads were trimmed by removing Illumina adapters sequences and low-quality bases using Homer tools (v4.7)
ChiP-seq reads were aligned to hg38 reference genome using Bowtie2 (v2.2.4)
Peak calling was performed using MACS2
peaks of individual replicates were combined in one peak file.
Genome_build: hg38
Supplementary_files_format_and_content: .txt files containing normalised and annotated peaks
|
| |
|
| Submission date |
Feb 03, 2021 |
| Last update date |
May 08, 2024 |
| Contact name |
Gino Nardocci |
| E-mail(s) |
gnardo@gmail.com
|
| Organization name |
Universidad de los Andes
|
| Street address |
Av. Mons. Álvaro del Portillo 12.455
|
| City |
Santiago |
| ZIP/Postal code |
7620001 |
| Country |
Chile |
| |
|
| Platform ID |
GPL15433 |
| Series (2) |
| GSE166098 |
HMGN5, an RNA and Nucleosome binding protein required for chromatin de-condensation and gene activation [ChIP-seq] |
| GSE166103 |
HMGN5, an RNA and Nucleosome binding protein required for chromatin de-condensation and gene activation |
|
| Relations |
| BioSample |
SAMN17769424 |
| SRA |
SRX10012803 |
