|
| Status |
Public on Dec 10, 2021 |
| Title |
Mother Ind.1 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood mononuclear cell
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Healthy
family: Ind.1 Mother
cell type: Peripheral blood mononuclear cell
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed and chromatin was fragmented with Micrococcal nuclease (MNase) and incubuated with 2 mg of anti-H3K27ac (39133, Active Motif) for immunoprecipitation
Libraries were prepared as follows. 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 ~300 bp (insert plus adaptor and PCR primer sequences) were purified by double-sided SPRI size selection . The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were send to a sequencing platform core facility and sequenced on a Next-seq 500 (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Single-end reads were mapped to the hg19 genome by the BWA algorithm and duplicate reads (read-pairs mapping to the same genomic location) were collapsed. Reads mapped to non-canonical and mitochondrial chromosomes were also removed. For each sample, ChIP-seq peaks were detected using MACS2 standard parameters, and peaks were selected only if they are present in both duplicates
Genome_build: hg19
Supplementary_files_format_and_content: Peaks files are generated using MACS2
|
| |
|
| Submission date |
Dec 07, 2021 |
| Last update date |
Dec 11, 2021 |
| Contact name |
Alice Mollé |
| E-mail(s) |
alice.molle@univ-nantes.fr
|
| Organization name |
University of Nantes
|
| Lab |
Center for Research in Transplantation and Immunology (CRTI)
|
| Street address |
30 bd Jean Monnet
|
| City |
Nantes |
| ZIP/Postal code |
44093 |
| Country |
France |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE190394 |
Rare germline heterozygous missense variants of the BRCA1-Associated Protein 1 gene, BAP1, heterozygous missense variants cause a syndromic neurodevelopmental disorder |
|
| Relations |
| BioSample |
SAMN23744448 |
| SRA |
SRX13343650 |
