|
| Status |
Public on Mar 13, 2017 |
| Title |
GFP-H3.Y replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa (Kyoto), GFP-H3.Y ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa (Kyoto)
transfected plasmid: pIRESneo-EGFP
chip antibody: GFP (Abcam, ab290, lot GR278073-1)
|
| Treatment protocol |
NA
|
| Growth protocol |
Hela Kyoto (HK) cells were grown in DMEM (Sigma) supplemented with 10% fetal calf serum (FCS; Sigma) and 1% penicillin/streptomycin at 37°C and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
HeLa Kyoto cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclear lysates were subjected to chromatin shearing to an average size of 150 bp. Histone-DNA complexes were isolated with GFP-antibody.
All libraries were prepared with the MicroPlex library preparation kit v2 (order no C05010012) following manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
GFP-H3.Y_rep_1
pIRESneo-EGFP (generated from pIRESneo (digested with EcoRV and BamHI) with the EGFP insert from pEGFP-C1 (digested with NheI followed by Klenow reaction and subsequently digested with BamHI)).
|
| Data processing |
Quality control was done using FASTQC.
Removal of low quality reads and adapters was done by trim_galore.
Alignment was done with bowtie2-2.0.0-beta6 with parameters -p 6 -D 15 -R 2 -N 0 -L 32 -i S,1,0.75 -M 10000.
Duplicate reads were removed with Samtools' rmdup function.
Peak calling was performed with Macs2 callpeak function.
Coverage vectors were extracted with deeptools' bamCoverage function.
Additional processing was done in R/BioConductor. Peaks separated by less then 2 kb were stitched together.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Coverage vectors from bamCoverage are stored as bigwig files.
Supplementary_files_format_and_content: Genomic intervals of binding peaks are stored as BED format files.
|
| |
|
| Submission date |
Jan 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Marek Bartkuhn |
| E-mail(s) |
marek.bartkuhn@gen.bio.uni-giessen.de
|
| Organization name |
Justus-Liebig-University Giessen
|
| Department |
Biomedical Informatics and Systems Medicine
|
| Street address |
Aulweg 132
|
| City |
Giessen |
| State/province |
Hessen |
| ZIP/Postal code |
35392 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE94034 |
H3.Y discriminates between HIRA and DAXX chaperone complexes and reveals unexpected insights into human DAXX-H3.3-H4 binding and deposition requirements |
|
| Relations |
| BioSample |
SAMN06256463 |
| SRA |
SRX2514373 |
