|
| Status |
Public on Jun 04, 2014 |
| Title |
TET1-FL |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T cell
|
| Organism |
Homo sapiens |
| Characteristics |
transfection: TET1-FL expression plasmid
cell line: HEK293T
|
| Treatment protocol |
mTET1-CD, TET1-CD, mTET1-FL, TET1-FL expression plasmid or empty vector was transfected into HEK293T cells by using OPTI-MEM (Invitrogen) and FuGene HD transfection reagent (Roche). Three days after transfection, overexpressed cells were purified with fluorescent activated cell sortng.
|
| Growth protocol |
HEK293T cells were cultured in Dulbecco's Modified Eagle Medium modified with 10% fetal bovine serum and 100 μg/ml streptomycin-penicillin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Libraries were prepared from 100 ng of DNase-treated total RNA samples using Encore® Complete RNA-Seq Library System (NuGEN, San Carlos, CA) following the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The reads were mapped to human genome (hg19) by TopHat (V2.0.5)
The number of fragments in each known gene from RefSeq database was enumerated using htseq-count from HTSeq package.
The differential expression between samples was statistically accessed by R/Bioconductor package edgeR (V3.0.8) and DESeq (V1.10.1), using the two most similar samples (mTET1-FL and TET1-FL) to estimate the biological variation. Genes with FDR≤0.05 by both edgeR and DESeq and fold change≥2 were called significant.
Genome_build: hg19
Supplementary_files_format_and_content: _fpkm.txt: the FPKM value (fragments per kilobase of exon per million fragments mapped) for each gene. Only genes with >=10 fragments in at least one sample and with no isoform shorter than 200bp are reported.
Supplementary_files_format_and_content: _DE.txt: the significant differentially expressed genes.
|
| |
|
| Submission date |
Aug 13, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
CHUNLEI JIN |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Texas MD Anderson Cancer Center
|
| Street address |
1515 Holcombe Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE44039 |
TET1 is a maintenance DNA demethylase that prevents methylation spreading in adult cells |
| GSE49833 |
TET1 is a maintenance DNA demethylase that prevents methylation spreading in adult cells [RNA-seq] |
|
| Relations |
| BioSample |
SAMN02316415 |
| SRA |
SRX334224 |
