 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 18, 2014 |
| Title |
Caco-2 RNC-mRNA |
| Sample type |
SRA |
| |
|
| Source name |
Caco-2 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Caco-2
sample type: RNC-mRNA
|
| Growth protocol |
Human Caco-2 cells were obtained from American Type Culture Collections (ATCC, Rockville, MD). Cells were cultured in complete DMEM media (Invitrogen, Carlsbad, CA), supplemented with 10% fetal bovine serum (FBS) (PAA Australia, Weike Biochemical Reagent, Shanghai, China), 1% penicillin/streptomycin and 10 μg/mL ciprofloxacin.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
See the paper " Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific" Wang et. Al. NAR 2013. Briefly, the polyA+ mRNA in the total mRNA or RNC-mRNA samples was isolated using the RNA Purification Beads (Illumina). The mRNA was fragmented by incubation in Elute-Prime-Fragment Mix at 94°C for 8 min to obtain 120–200 bp inserts
See the paper " Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific" Wang et. Al. NAR 2013. Briefly, the polyA+ mRNA in the total mRNA or RNC-mRNA samples was isolated using the RNA Purification Beads (Illumina). The mRNA was fragmented by incubation in Elute-Prime-Fragment Mix at 94°C for 8 min to obtain 120–200 bp inserts. First-strand cDNA was synthesized with SuperScript II Reverse Transcriptase (Invitrogen) using random primer, and Ampure XP beads (Beckman Coulter, Beijing, China) were used to isolate double-stranded cDNA synthesized by Second Strand Master Mix. The adapters were ligated to the A-Tailing fragment, and 12 cycles of PCR were performed to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Invitrogen) and validated by Agilent 2100 bioanalyzer (Agilent, Beijing, China). Clusters were generated by cBot with the library diluted to 10 pM
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
polyA+ mRNA from RNC-RNA
|
| Data processing |
High quality reads which passed the Illumina filter were mapped with FANSe2 algorithm (http://bioinformatics.jnu.edu.cn/software/fanse2/) with the parameters –L55 –E5 –U0 –S10
Reference sequence: NCBI RefSeq-RNA reference sequence (downloaded from from http://hgdownload.cse.ucsc.edu/downloads, accessed on Jan. 21st, 2013)
Genome_build: hg19
Supplementary_files_format_and_content: Caco-2 rpkM: rpkM of mRNA and RNC-mRNA
|
| |
|
| Submission date |
Jul 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Gong Zhang |
| E-mail(s) |
zhanggong@jnu.edu.cn
|
| Organization name |
Jinan University
|
| Department |
Institute of Life and Health Engineering
|
| Lab |
Translatomics Lab
|
| Street address |
Huang-Pu Avenue West 601
|
| City |
Guangzhou |
| ZIP/Postal code |
510632 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE48603 |
Transcriptome and Translatome Profiling of Caco-2 cells |
|
| Relations |
| BioSample |
SAMN02228227 |
| SRA |
SRX318855 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
