|
| Status |
Public on Dec 07, 2020 |
| Title |
RNAi of NF-YB RNA-seq Replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
treatment: NF-YB siRNA J-010002-08-0002
|
| Treatment protocol |
Cells at 25-30% confluence were transfected with 50 nM siRNA using 3.75 µL Lipofectamine 3000 Reagent (ThermoFisher) in 1.5 mL final volume of Optimem (ThermoFischer) per well.
|
| Growth protocol |
HeLa cells were grown in DMEM high glucose with L-glutamine (EuroClone SpA) supplemented with 10% FBS, 100 U/mL penicillin and 100 µg/mL streptomycin. The day before transfection, 0.15 × 10e6 cells/well were seeded in antibiotic-free medium in a 6-well plate.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The RNAs were extracted using TRI-reagent (Merck) and further purified with RNeasy Mini Kit (Qiagen) following the RNA clean-up protocol.
Performed by Novogene. Total RNAs were poly-T purified, randomly fragmented and transformed in cDNA with NEB library preparation protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Alignment performed with bowtie2 within rsem-calculate-expression against hg19 transcriptome.
Gene quantification performed with rsem-calculate-expression.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.genes.results.txt: Tab-delimited text files containing gene expression as counts, TPM and FPKM for each sample.
|
| |
|
| Submission date |
May 26, 2020 |
| Last update date |
Dec 08, 2020 |
| Contact name |
Diletta Dolfini |
| E-mail(s) |
diletta.dolfini@unimi.it
|
| Organization name |
University of Milan
|
| Department |
Bioscience
|
| Street address |
Via Celoria, 26
|
| City |
Milano |
| State/province |
MI |
| ZIP/Postal code |
20133 |
| Country |
Italy |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE151237 |
On the NF-Y regulome as in ENCODE (2019) |
|
| Relations |
| BioSample |
SAMN15028111 |
| SRA |
SRX8402223 |
