|
| Status |
Public on Jan 01, 2013 |
| Title |
Input_CT18_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Liver tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Liver
chip antibody: None
time point: CT18
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was sheared using a Diagenode Bioruptor at 4oC, using conditions optimised to produce 150-300bp fragments with the use of 15 ml Falcon tubes holding 2ml of lysate each (30 cycles of 30 secs on HIGH, 30 secs OFF). Sheared chromatin was transferred to 1.5 ml microcentrifuge tubes and spun at 14,000 rpm for 15 min at 4°C to pellet debris. Cleared supernatants were transferred to clean microcentrifuge tubes and 100 µl from each sample lysate was saved for use as an input control for sequencing and to check fragment size distribution. standard Illumina indexing primers were used, as per the manufacturer’s instructions. All libraries were multiplexed, and 4 indexed pooled samples (corresponding to four time-points, CT0, 6, 12, 18) sequenced per lane.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Chromatin IP against Input
|
| Data processing |
Raw paired-end 50bp reads (in FASTQ format) were aligned to the UCSC mm9 genome build with Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) using pre-built indexes downloaded from the host website. Parameters were optimised to utilise the software’s multi-threading capabilities (we typically used a 128-core cluster for alignments). Alignment files were then converted from the standard Bowtie output format to ALN files (for use with Cisgenome) using a custom Perl script. Alignments were then analysed using a 2-sample comparison (ChIPed sample vs. Input control for each time-point) with Cisgenome v1, using a cut-off false discovery rate of 10% and a sliding window size of 100. Output files were converted into various formats for browsing datasets and to display data. The Cisgenome and UCSC browsers were used for data visualisation, using custom tracks
|
| |
|
| Submission date |
Apr 18, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Utham Kashyap Valekunja |
| Organization name |
Smilow Center for Translational Research
|
| Department |
Department of Systems Pharmacology & Therapeutics, Perelman School of Medicine, University of Pennsylvania
|
| Street address |
10-179/180 Lab, 3400 Civic Center Boulevard, Building 421
|
| City |
Philadelphia |
| ZIP/Postal code |
PA 19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE37393 |
Daily cycling of genome-wide histone methylation |
| GSE37396 |
The histone methyltransferase MLL3 regulates genome-scale circadian transcription |
|
| Relations |
| SRA |
SRX143298 |
| BioSample |
SAMN00858150 |
