|
| Status |
Public on Nov 04, 2012 |
| Title |
mRNA 3mM sodium bicarbonate |
| Sample type |
SRA |
| |
|
| Source name |
mRNA 3mM sodium bicarbonate
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: none
agent: 3mM sodium bicarbonate
cell line: HeLa
|
| Treatment protocol |
Cells were plated in 10-cm dishes and allowed to attach overnight. The following day the culture medium was replaced with DMEM (Sigma #D5030 supplemented with glucose, glutamine and pyruvate) with either 25 mM or 3 mM sodium bicarbonate which resulted in a medium pH of 7.4 and 6.5, respectively.
|
| Growth protocol |
Cells were routinely cultured in DMEM (Cellgro) that was supplemented with 10% FBS (Hyclone) and 1X antibiotic/antimycotic (Gibco). Cells were passaged every 2-3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from HeLa cells grown in 25 or 3 mM sodium bicarbonate using Qiagen easy RNA kit. Maximum amount of RNA was used to start the library preparation according to the manufacturer's instructions (Illumina). Libraries were sequenced using Illumina HIseq-2000 to obtain 50 bp-long reads. Nugen Ovation Ultralow Library system
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mRNA-seq pH 6.5
|
| Data processing |
Alignment of mRNA-seq reads was performed using default parameters of Tophat.
Aligned reads were converted to sam format and SAMMate software6 was used to determine the transcript RPKM (reads per kilobase of exon per million of reads).
Genome_build: hg19
Supplementary_files_format_and_content: bed, RPKM.txt
|
| |
|
| Submission date |
Aug 14, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Siavash K Kurdistani |
| E-mail(s) |
Skurdistani@mednet.ucla.edu
|
| Organization name |
UCLA
|
| Department |
Biological Chemistry
|
| Lab |
Kurdistani
|
| Street address |
615 Charles E Young Dr South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE40114 |
Histone acetylation regulates intracellular pH |
|
| Relations |
| SRA |
SRX176647 |
| BioSample |
SAMN01113279 |
