|
| Status |
Public on Jul 24, 2016 |
| Title |
siBP3 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cell lines
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Hela
tissue: cervical carcinoma
age: immortal
genotype: siBP3
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Cells were grown until 70% confluency, and then transiently transfected with siRNAs using Lipofectamine RNAiMax reagent according to manufacturer’s protocol (Thermofisher Scientic). Second siRNA transfection were done 48 hours later. Cells then were harvested after 48 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol® reagent following the manufacturer’s protocol (Thermofisher Scientic)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls were performed using CASAVA (v. 1.8.2)
Sequence libraries were filtered for adapter contamination using cutadapt (v1.8.3)
Filtered reads were aligned to hg19 geneome assembly using Bowtie (v.2.2.5)
Counted the siBP3 and control samples mapped readsin the annotated transcripts regions using featurecounts(v1.4.6) module from subread package. Counts were normalized to library size
Differential expression analysis was performed using edgeR bioconductor package (v.3.8.6)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count per million values for each Sample
|
| |
|
| Submission date |
Feb 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ralf Kittler |
| E-mail(s) |
Ralf.Kittler@UTSouthwestern.edu
|
| Organization name |
University of Texas Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE77855 |
HP1BP3, a chromatin retention factor for co-transcriptional microRNA processing (miRNA-Seq) |
| GSE77856 |
HP1BP3, a chromatin retention factor for co-transcriptional microRNA processing |
|
| Relations |
| SRA |
SRX1581954 |
| BioSample |
SAMN04501343 |
