|
| Status |
Public on Jul 15, 2019 |
| Title |
U2OS_WT_Suzcom_1 |
| Sample type |
SRA |
| |
|
| Source name |
osteosarcoma-derived cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: ipNF05.5
genotype: WT
chip antibody: Suz12
|
| Growth protocol |
ipNF05.5 cells were cultured in DMEM media supplemented with 10% FBS and 1% L-Glutamine and 1% non essential amino acids.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared according to Illumina's DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
ChIP-Seq/CUT&RUN
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were mapped to the concatenated human reference genome (GRCh37/hg19) and Drosophila melanogaster (dm6) with Bowtie2 (2.2.9) using the following parameters: --very-sensitive --end-to-end --reorder.
PCR duplicates were removed with Picard Tools MarkDuplicates (1.97)
BAM files were filtered exclude artifact regions. The merged consensus blacklist was obtained from the Kundaje lab at Stanford University (Stanford, CA, USA).
Reads were extended to 200bp and RPKM normalized counting only reads in bins of length 50 and converted to bigWig format using DeepTools (2.4.1).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Apr 26, 2019 |
| Last update date |
Jul 15, 2019 |
| Contact name |
Nicolas Servant |
| E-mail(s) |
[email protected]
|
| Organization name |
Institut Curie
|
| Street address |
26 rue d'ulm
|
| City |
Paris Cedex 05 |
| ZIP/Postal code |
75248 |
| Country |
France |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE130230 |
EZHIP constrains Polycomb Repressive Complex 2 activity in germ cells (ChIP-Seq) |
| GSE130231 |
EZHIP constrains Polycomb Repressive Complex 2 activity in germ cells |
|
| Relations |
| BioSample |
SAMN11518963 |
| SRA |
SRX5759193 |
