|
| Status |
Public on Dec 06, 2017 |
| Title |
OE Cntl-NE-1_nuclear_RNA |
| Sample type |
SRA |
| |
|
| Source name |
uterine cervix
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
tissue: uterine cervix
genotype/variation: control
rna fraction: rRNA-depleted nuclear RNA
|
| Treatment protocol |
For overexpression, DNA transfections were carried out with Lipofectamine2000(Invitrogen) for 24 hr.
|
| Growth protocol |
HeLa cells were cultured in DMEM supplemented with 10% FBS (Biochrom).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from HeLa with TRIzol (Invitrogen). 1ug of nuclear RNA was depleted with rRNA and constructed sequencing libraries.
Libraries were generated with TruSeq Stranded Total RNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
rRNA-depleted nuclear RNA
|
| Data processing |
Basecalls performed using TopHat2.0,fastx_toolkit-0.0.13.2 (Q33)
RNA-seq reads were cleaned and mapped the human genome (hg19 version) TopHat2.0. Reads mapping to multiple independent genomic locations were assigned to the most abundant biotype of the locations. Genome annotations from RefSeq and ENSEMBL were downloaded from the UCSC genome browser website, and supplemented with published datasets.
To compare the expression of individual RNAs, we calculated the corrected reads per million (RPM) of each transcript. Fold changes were computed from the average normalized read coverage per million bases for ensemble gene.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include RPM values for each Sample
|
| |
|
| Submission date |
Jul 09, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Hong Cheng |
| E-mail(s) |
hcheng@sibcb.ac.cn
|
| Organization name |
Shanghai Institutes for Biological Sciences
|
| Department |
Shanghai Institute of Biochemistry and Cell Biology
|
| Lab |
StateKey Laboratory of Molecular Biology
|
| Street address |
320 YueYang Road
|
| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE77641 |
hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export |
| GSE100982 |
hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export VI |
|
| Relations |
| BioSample |
SAMN07337631 |
| SRA |
SRX2992320 |
