|
|
| Status |
Public on Jun 03, 2020 |
| Title |
K562 RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
K562 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
cell type: erythrocyte
|
| Growth protocol |
the cells were grown at 37 C/5% CO2 in DMEM supplemented with 10% FBS/1% Pen-strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
whole RNA was extracted from 1 T-25 flask using the Qiagen Rneasy Kit, according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls were performed with CASAVA version 1.8.2
75bp paired end reads were aligned to the GRCh38.p13 genome and transcriptome annotations using tophat version 2.1.1 with default parameters
Gene expression was quantified using cufflinks version 2.2.2 with the cuffdiff command using the GRCh38.p13 transcriptome as reference and default parameters.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited file which contains FPKM values and statistical comparison between K562 and Molt4 gene expression
|
| |
|
| Submission date |
Apr 10, 2020 |
| Last update date |
Jun 03, 2020 |
| Contact name |
Sarah A Slavoff |
| E-mail(s) |
sarah.slavoff@yale.edu
|
| Phone |
2037378670
|
| Organization name |
Yale University- West Campus
|
| Department |
Chemistry
|
| Lab |
Slavoff Lab
|
| Street address |
Yale University West Campus-Building 600
|
| City |
West Haven |
| State/province |
Connecticut |
| ZIP/Postal code |
06516 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE148451 |
RNA sequencing of K562 and MOLT4 cell lines |
|
| Relations |
| BioSample |
SAMN14573354 |
| SRA |
SRX8094426 |
