|
| Status |
Public on Dec 06, 2023 |
| Title |
Ctrl rep1 |
| Sample type |
SRA |
| |
|
| Source name |
CCRF-CEM
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CCRF-CEM
cell type: T cell leukemia
genotype: CCRF-CEM/HA-AMPKa2
treatment: No treatment
|
| Treatment protocol |
Cells were grown in ctrl or no glucose medium for 24 hours.
|
| Growth protocol |
CCRF-CEM/HA-AMPKa2 cells were grown in RPMI + 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cells using the RNeasy plus kit (Qiagen).
Libraries were prepared using Illumina’s TruSeq Stranded Total RNA library preparation kit. Libraries were sequenced on a 75 bp single-end run using the NextSeq 500 High-Output Kit (75-cycle; 400 M flow cell).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned to the hg38 transcriptome and ERCC spike-in indexes using RSEM (v1.3.0) and STAR (v2.6.0c) with Gencode annotations.
Differentially expressed genes were determined by DESeq2 (v1.18.1, Fold Change > 1.5 or < -1.5, q value < 0.05) after gene counts were corrected based on ERCC variances using RUVseq (v1.12.0).
Supplementary files format and content: hg38
Supplementary files format and content: data_matrix_ctrl_no_glucose.txt: Matrix table for all genes expression.
|
| |
|
| Submission date |
Aug 01, 2022 |
| Last update date |
Dec 06, 2023 |
| Contact name |
Julio C Barredo |
| Organization name |
University of Miami
|
| Street address |
1580 NW 10th ave room
|
| City |
MIAMI |
| State/province |
Florida |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE210212 |
Metabolic stress induces gene reprograming in ALL cells [RNA-seq] |
| GSE210214 |
AMPK directly regulate a subset of genes expression in ALL cells |
|
| Relations |
| BioSample |
SAMN30079165 |
| SRA |
SRX16750430 |
