|
| Status |
Public on Oct 31, 2018 |
| Title |
Ribominus total RNAseq whole cell 2 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Ribominus total RNAseq whole cell
|
| Growth protocol |
Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and pennicilin/streptomycin antibiotics at 37˚C with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested and RNA was extracted using the TRIZol. Genomic DNA was digested with DNaseI. rRNA was removed with the RiboMinus Kit.
Library was prepared using NEBNext mRNA Sample Prep Master Mix Set kit (NEB).
TRU-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
WT Replicate B
|
| Data processing |
Adaptor sequences were trimmed from reads using Flexbar
RNA-seq reads were aligned to hg19 using Tophat v2.0.0 coupled with Bowtie v1.1.1
Reads were counted into features using samtools with (-c) option. Bedcoverage tool was used to count reads into transcripts.
RPKM values were calculated using the formula: counts * 10^9 / length of feature * total mapped reads.
Genome_build: hg19
Supplementary_files_format_and_content: Bed file containing RPKM values of lincRNAs and protein-coding transcripts.
|
| |
|
| Submission date |
Apr 27, 2018 |
| Last update date |
Oct 31, 2018 |
| Contact name |
Michaela Müller-McNicoll |
| E-mail(s) |
mueller-mcnicoll@bio.uni-frankfurt.de
|
| Phone |
+49 69 798 42079
|
| Organization name |
Goethe University Frankfurt
|
| Department |
Institute for Cell Biology and Neuroscience
|
| Lab |
RNA Regulation Group
|
| Street address |
Max-von-Laue-Str. 13
|
| City |
Frankfurt am Main |
| ZIP/Postal code |
60438 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE113812 |
WT HeLa total RNA-seq (RiboMinus) |
| GSE113814 |
Transcriptome-wide mapping of RNA:protein interactions of three SR proteins in HeLa cells |
|
| Relations |
| BioSample |
SAMN08996245 |
| SRA |
SRX4004955 |
