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Sample GSM3734222 Query DataSets for GSM3734222
Status Public on Jul 15, 2019
Title U2OS_WT-2-IgG
Sample type SRA
Source name osteosarcoma-derived cell line
Organism Homo sapiens
Characteristics cell type: ipNF05.5
genotype: WT
chip antibody: IgG
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.
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 23, 2019
Last update date Jul 15, 2019
Contact name Nicolas Servant
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
BioSample SAMN11484336
SRA SRX5727032

Supplementary file Size Download File type/resource 124.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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