|
| Status |
Public on Apr 28, 2017 |
| Title |
K562-CEBPα-ER β-estradiol 3 |
| Sample type |
SRA |
| |
|
| Source name |
K562 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: K562 cells stabely expressing C/EBPalpha-ER fusion protein
agent: beta-estradiol
|
| Treatment protocol |
Cells were treated with 5µM β-estradiol to activate C/EBPα
|
| Growth protocol |
Cells were grown in RPMI-1640 medium without phenolred, 10% charcoal treated FBS, 1% Pen/Strep and 1µg/ml Puromycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol method according to the manufacturer's instructions
500ng total RNA extracted using Trizol method was used for small RNA library preparation with the TruSeq™ Small RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions. The barcoded libraries were size restricted between 140 and 165 bp, purified and quantified using the Library Quantification Kit-Illumina/Universal (KAPA Biosystems) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
Demultiplexing all 50-bp reads from each lane using the CASAVA v1.8.2 software (Illumina)
Adaptor sequences were trimmed from raw sequences using cutadapt software
From the remaining sequences, only reads 15–27 bases long were kept for analysis
Alignment of reads to human (hsa-only) mature sequences of miRBase (5–8) v17 was done using the bowtie aligner
Mapped reads for each miRNA were counted with R/Bioconductor programming environment by application of the ShortRead library
Supplementary_files_format_and_content: abundance measurements
|
| |
|
| Submission date |
Sep 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Gerhard Behre |
| Organization name |
University of Leipzig
|
| Department |
Hematology and Oncology
|
| Street address |
Johannisallee 32a
|
| City |
Leipzig |
| ZIP/Postal code |
04103 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15456 |
| Series (1) |
| GSE72634 |
C/EBPalpha regulated microRNA expression profiling in inducible K562-C/EBPalpha-ER cells |
|
| Relations |
| BioSample |
SAMN04027069 |
| SRA |
SRX1178180 |
