|
| Status |
Public on Jun 10, 2015 |
| Title |
K562_CEBPA_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
K562 CEBPA cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: leukemia cell line
cell line: K562
treatment: CEBPA induction
|
| Treatment protocol |
Doxycycline (Dox) were purchased from Sigma and utilized at a concentration of 200 ng/ml for 48 hours
|
| Growth protocol |
K562 cell lines were cultured at 37°C under an atmosphere containing 5% CO2 in RPMI 1640 medium supplemented with 1x Penicillin/Streptomicin solution, 1x L-glutamine and 10% Fetal Bovine Serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the Rneasy kit (Qiiagen)
Libraries were prepared for sequencing using standard Illumina protocol accompanying TruSeq stranded mRNA sample prep kit (RS-122-2101)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
Seq-reads were aligned to the hg19 human assembly using TopHat 2.0 with parameters -p -o -G read-edit-dist 4 --read-gap-length 2 --read-mismatches 2 --read-realign-edit-dist 1 --library-type fr-firststrand --min-intron-length 50 --max-intron-length 300000
Transcripts were assembled with Cufllinks 2.2 using Gencode v.19 with parameters -o output --frag-bias-correct dirhg19.fa --multi-read-correct -G dirgencode.v19.annotation.gtf --compatible-hits-norm --library-type fr-firststrand --max-bundle-frags 500000 -p 8 -q
Diffreential expression was assessed using CuffDiff
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Jan 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Alessandro Fatica |
| E-mail(s) |
alessandro.fatica@uniroma1.it
|
| Organization name |
Sapienza University of Rome
|
| Department |
Biology and Biotechnology "C. Darwin"
|
| Street address |
P.le Aldo Moro 5
|
| City |
Rome |
| ZIP/Postal code |
00185 |
| Country |
Italy |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE65235 |
Identification of transcripts regulated by CEBPA protein and its P30 isoform in K562 |
|
| Relations |
| BioSample |
SAMN03292389 |
| SRA |
SRX851822 |
