|
| Status |
Public on May 01, 2015 |
| Title |
SMCHD1_ChIPseq_HCT116 |
| Sample type |
SRA |
| |
|
| Source name |
HCT-116
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT-116
cell type: Colon carcinoma cells
chip antibody: Anti-SMCHD1 Rabbit polyclonal IgG
chip antibody vendor: Sigma-Aldrich
chip antibody cat. #: HPA039441
chip antibody lot #: R36066
|
| Growth protocol |
Cells were cultured in McCoy medium with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiment was performed using formaldehyde-crosslinked chromatin from HCT116 cells (human carcinoma cell line) and antibody against SMCHD1 protein. Non-specific rabbit polyclonal IgG was used in control experiment.
Libraries were prepared by Fasteris SA (Switzerland) and were sequenced on HiSeq2000.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base-calling performed by Fasteris SA (CASAVA pipeline v.1.8.2)
50 nt-long sequenced reads were mapped onto the sequence genome of Homo sapiens (hg19 assembly) according to sequencing quality using Bowtie.
For genome-wide enrichment analysis, only reads perfectly matching the human genome were retrieved (one mismatch was nevertheless allowed on low-quality nucleotides using –e 20 option). Redundant reads as well as reads mapping to multiple genomic locations were also discarded.
Enrichment peaks were called using SISSRs v 1.4 (Jothi et al., 2008) with default parameters using input DNA as background. Peaks corresponding to repetitive regions were discarded using BEDTools (Quinlan & Hall, 2010) (satellites 2/3, alpha/beta satellites and ribosomal DNAs genomic positions were retrieved from the UCSC repeatmasker track (http://genome.ucsc.edu/)) as well as peaks identified in IgG control library.
Annotation of the identified peaks as well as peak overlap and motif discovery were performed using HOMER tool suite (Heinz et al., 2010)
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were generated using HOMER tool suite (Heinz et al., 2010) and represent normalized fragment density profile (based on genome-unique unredundant perfectly mapping reads). BED files contain coordinates (chromosome, start and end) of called peaks.
|
| |
|
| Submission date |
Apr 29, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jérôme Déjardin |
| E-mail(s) |
jerome.dejardin@igh.cnrs.fr
|
| Organization name |
Institute of Human Genetics
|
| Lab |
Biology of Repetitive Sequences
|
| Street address |
141, rue de la Cardonille
|
| City |
MONTPELLIER CEDEX 5 |
| ZIP/Postal code |
34396 |
| Country |
France |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE46462 |
The role of SMCHD1 in the formation of constitutive heterochromatin |
|
| Relations |
| BioSample |
SAMN02086221 |
| SRA |
SRX272438 |
| Named Annotation |
GSM1130654_SMCHD1_HCT116_hg19.bigWig |
