|
| Status |
Public on Jun 01, 2020 |
| Title |
(+)siC_4 FGC1198_s_2 |
| Sample type |
SRA |
| |
|
| Source name |
AML12 cells (ATCC® CRL-2254™)
|
| Organism |
Mus musculus |
| Characteristics |
strain: AML12
|
| Treatment protocol |
RNA-Seq: AML 12 cells were cultured in 10% FBS (FBS(+)) or had withdrawal of serum 24 hours before harvest (FBS(-)). 45 hours before harvest, AML 12, HepG2 and SK-Hep-1 cells were treated with control or cyclin D1 siRNA (Dharmacon On-Target plus SMARTpool, catalog # L-042441-00-0020).
ChIP-Seq: Mice were treated with recombinant adenoviruses as above.
|
| Growth protocol |
RNA-Seq: AML12, HepG2, and Sk-Hep1 cells were cultured in the presence or absence of serum along with control or cyclin D1 siRNA (see PMID 27351284 and 22751438 for the culture conditions). HepG2 and SK-HEP-1 cells were cultured in the presence of control or cyclin D1 siRNA (see PMID 27351284 for the culture conditions)
ChIP-Seq: Male BALB/c mice were transduced with recombinant adenoviruses encoding cyclin D1-HA-FLAG or cyclin D1-RD-FLAG (see PMID: 22751438 and 27351284 for details). Livers were harvested 24 hours later for ChIP-seq.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-Seq: RNA was extracted using Qiazol followed by purification using the miRNeasy kit (Qiagen)
ChIP-Seq: DNA was exgtracted from mouse liver as previously described (PMID: 18556755).
RNA-Seq: Libraries were prepared using TruSeq Stranded mRNA HT kit using standard Illumina protocols
ChIP-Seq: Libraries were prepared using NEBNext ChIP-seq library prep reagent kit according to Illumina's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
FBS(+) Control siRNA rep-4
(+)siC_4
RawTranscriptCounts_AML12.xls
|
| Data processing |
Illumina's bcl2fastq-v2.17.1.14 software was used to convert BCL basecall files to fastq files.
RNA-Seq: Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to respective genomes and Refseq transcriptome. Differential expression analysis was carried out using a custom script implementing EdgeR software.
ChIP-Seq: Reads were aligned to mm9 genome using bowtie version 0.12.7 with parameters -v 3 -k 1 -m 1 --best --strata. Redundant reads were discarded before creating bedgraph profiles.
ChIP-Seq: Peak calling on HNF4a ChIP samples was done using HOMER in factor mode and FDR cut off of 0.01 with respect to corresponding Input. Bioconductor's diffBind package was used for differential binding analysis.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: Excel file with raw transcript counts
Supplementary_files_format_and_content: Tab-delimited peak files listing genomic coordinates and their respective scores and p-values. Scores represent fold-change with respect to Input.
|
| |
|
| Submission date |
Feb 27, 2020 |
| Last update date |
Jun 01, 2020 |
| Contact name |
Jeffrey H Albrecht |
| E-mail(s) |
albre010@umn.edu
|
| Organization name |
University of Minnesota
|
| Department |
Medicine - Gastroenterology
|
| Street address |
One Veterans Drive
|
| City |
Miinneapolis |
| State/province |
MN |
| ZIP/Postal code |
55417 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE146053 |
A negative reciprocal regulatory axis between cyclin D1 and HNF4α modulates cell cycle progression and metabolism in the liver |
|
| Relations |
| BioSample |
SAMN14237635 |
| SRA |
SRX7814929 |
