|
| Status |
Public on Apr 12, 2017 |
| Title |
4C_CT18 rep3 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: liver
age: 8 weeks
|
| Treatment protocol |
Three WT mice were sacrificed at CT6 and CT18 respectively after at least one week entrainment.
|
| Growth protocol |
The mice were housed under a 12-h light/12-h dark regimen with food and water available ad libitum for one week before being switched to complete darkness. The mice were switched to complete darkness two days before execution. CT0 is defined as the time when the lights are turned on.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For 4C libraray construction, nuclei were digested overnight by 800U HindIII (New England Biolabs) at 37°C with shaking. After inactivation by 1.6% (final concentration) of SDS at 65°C for 20 min, samples were washed and re-suspended in ligation buffer and ligated by 100U T4 DNA ligase (Thermo Fisher Scientific) at 16°C for 4 hr and then room temperature for 30 min. Ligated chromatin was digested by proteinase K before DNA purification. The purified DNA was further digested by DpnII (New England Biolabs) and then circularized using T4 DNA ligase (Thermo Fisher Scientific). After purification, 200 ng of DNA fromthe 4C library was used as the template for the PCR amplification using DyNAzyme EXT (Finn- zymes). Primers specific to bait region were applied for amplification by PCR. PCR products were used as the templates for a second PCR reaction utilizing the primers with the addition of Illumina adaptors.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
4C_CT18
|
| Data processing |
Library strategy: 4C-Seq
Fastq files containing raw sequence reads were aligned to mouse genome (mm9) by Tophat2. Then bedtools (v2.19.1) were applied to calculate the number of reads of each transcript based on the gene annotations from Ensembl annotation(v69). The reads numbers were normalized to reads per kilobase per million mapped reads (RPKM).
4C-seq fastq files were aligned to mouse genome (mm9) by Bowtie and others were aligned by Tophat2 and . Then bedtools (v2.19.1) were applied to calculate the number of reads of each transcript based on the gene annotations from Ensembl annotation(v69). The reads numbers were normalized to reads per kilobase per million mapped reads (RPKM).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values of genes for RNA-seq and reads count of HindIII fragments for 4C-seq.
|
| |
|
| Submission date |
Sep 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Zenghua Fan |
| Organization name |
University of California, San Francisco
|
| Street address |
1550 4th Street
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE87299 |
Transcriptome changes in mouse livers upon Bmal1 or Nr1d1 knock out and interactome of lnc-Crot by 4C-seq |
|
| Relations |
| Reanalyzed by |
GSE123131 |
| BioSample |
SAMN05818774 |
| SRA |
SRX2188152 |
