|
| Status |
Public on Aug 01, 2020 |
| Title |
AML37-Fx1-2 |
| Sample type |
SRA |
| |
|
| Source name |
AML37, primary cell-FX1
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: TP53
treatment: FX1 treated
cell type: Acute Myeloid Leukemia primary cells
|
| Treatment protocol |
Cells were treated for 12 hours using EC50 concentration for the same primary cell.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from ex vivo treatments was lysed with Trizol. After adding chloroform, lysates were centrifuged at 13000 G for 30minutes, and intermediate layer was harvested as DNA/ Protein-free RNA samples. They were cleaned up using RNeasy mini columns.
Illumina TruSeq stranded mRNA strand-specific library sequenced paired-end 50bp
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Frozen clinical samples, CD34-selected
|
| Data processing |
RNAseq fastq files were trimmed using Trim Galore and cutadapt to remove adapter sequences.
Trimmed fastq files were aligned using STAR (version 2.5.1b) to the human genome (hg19) using Gencode (version v19) transcriptome assembly.
Coding genes were quantified using subread featureCounts (v1.4.5-p1) using paired and strand-specific mode to annotate uniquely mapped reads to Gencode annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Gene counts and transcripts per million (TPM)
|
| |
|
| Submission date |
Jun 20, 2019 |
| Last update date |
Aug 01, 2020 |
| Contact name |
Cem Meydan |
| Organization name |
Weill Cornell Medical College
|
| Department |
Physiology & Biophysics
|
| Lab |
Melnick Lab & Mason Lab
|
| Street address |
1305 York
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE133112 |
BCL6 mediates Chemoresistance in Acute Myeloid Leukemia |
|
| Relations |
| BioSample |
SAMN12100578 |
| SRA |
SRX6099447 |
