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Sample GSM2688690 Query DataSets for GSM2688690
Status Public on Dec 06, 2017
Title OE Cntl-MTR4-IP-3
Sample type SRA
 
Source name uterine cervix
Organism Homo sapiens
Characteristics cell line: HeLa
tissue: uterine cervix
genotype/variation: control
rip antibody: anti-hMTR4 (ABclonal, catalog number A5576)
Treatment protocol For overexpression, DNA transfections were carried out with Lipofectamine 2000(Invitrogen) for 24 hr.
Growth protocol HeLa cells were cultured in DMEM supplemented with 10% FBS (Biochrom).
Extracted molecule total RNA
Extraction protocol RNAs associated with hMTR4 was isolated from HeLa with TRIzol (Invitrogen) .
stranded cDNA libraries were generated with TruSeq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions.
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model HiSeq X Ten
 
Description hMTR4 associated 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 excel files include RPM values for each Sample
 
Submission date Jun 28, 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
GSE100606 hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export V
Relations
BioSample SAMN07290287
SRA SRX2964703

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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