 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 28, 2020 |
| Title |
AD_67_manual_H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
S2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2
chip ab: H3K4me3 (Diagenode, C15410003, lot A5051-001P)
|
| Treatment protocol |
No treatment was applied
|
| Growth protocol |
S2 cells were cultured in Express Five SFM (Thermo Fisher Scientific) supplemented with glutamax, at 27 °C. HepG2 liver hepatocellular carcinoma (ATCC, HB-8065TM) were cultured in Eagle’s minimal essential medium (EMEM, Lonza, 06-174) supplemented with 10% fetal bovine serum (Sigma), 2 mM L-glutamine (Lonza), 1.8 mM CaCl2, 1 mM sodium pyruvate (Lonza) and penicillin–streptomycin mixture (100 units/mL, Lonza), at 37 °C at 5% CO2 in 10 cm plates, up to 70%-80% confluency.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
HepG2 and S2 cells were fixed in 1% methanol-free formaldehyde (Thermo Scientific, 28906) in D-MEM (for HepG2 cells) or Express Five SFM (for S2 cells) for 15 min at room temperature under gentle shaking. Formaldehyde was quenched for 5 min by adding 125 mM glycine final concentration. Cells were rinsed twice with ice-cold PBS, harvested by scraping (HepG2) and pelleted (300 g, 10 min, 4 °C). Cells were processed according to RELACS / AutoRELACS protocols
Libraries were prepared according to Illumina's instructions using NebNext Ultra II kit. After Illumina adapter ligation, library was PCR amplified. Fragments were size-selected to eliminate adapter dimers contamination using AMPure XP beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on NovaSeq 6000 machine, following manufacturer's protocol.
High-throughput RELACS ChIP-seq and automated high-throughput AutoRELACS ChIP-seq
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
fastq files were demultiplexed on RELACS barcodes and aligned to dm6 (S2 cells) or hg38 (HepG2) using snakePipes v. 1.2.3. QC metrics and further downstream files (bigwig) were also generated using snakePipes (Bhardwaj et al. 2019)
default parameters used for the analysis are available at https://github.com/FrancescoFerrari88/AutoRELACS/tree/master/snakePipes_defaults
Genome_build: dm6 (S2 cells) and hg38 (HepG2)
Supplementary_files_format_and_content: bigWig, normalized coverage
|
| |
|
| Submission date |
Mar 16, 2020 |
| Last update date |
Jul 29, 2020 |
| Contact name |
Thomas Manke |
| E-mail(s) |
manke@ie-freiburg.mpg.de
|
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
|
| Street address |
Stuebeweg 51
|
| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL25244 |
| Series (1) |
| GSE147042 |
AutoRELACS: Automated Generation And Analysis of Ultra-parallel ChIP-seq |
|
| Relations |
| BioSample |
SAMN14383516 |
| SRA |
SRX7917498 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4413492_AD_67_manual_H3K4me3.filtered.seq_depth_norm.bw |
5.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
