|
| Status |
Public on Mar 14, 2021 |
| Title |
AML1956_at_day_0_sample_2 |
| Sample type |
SRA |
| |
|
| Source name |
primary AML1956
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary AML1956
treatment: Control mice, untreated
|
| Treatment protocol |
PDX models were treated with AraC (Cytarabine) for 5 consecutive days with 60 mg/kg (i.p.).
|
| Growth protocol |
Patient-derived AML cells engrafted in NSG mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq libraries were prepared using the TruSeq RNA Kit according to the manufacturer
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to hg19 using STAR with default parameters
RNAseq fastq files were trimmed using Trim Galore and cutadapt to remove adapter sequences. Trimmed fastq files were aligned using STAR (version 2.5.3a) to the human genome (hg19) using Gencode (v19) transcriptome assembly. Coding genes were quantified using subread featureCounts (v1.4.5-p1) to annotate uniquely mapped reads to Gencode annotation.
Genome_build: hg19
Supplementary_files_format_and_content: FPKMs
|
| |
|
| Submission date |
Mar 06, 2020 |
| Last update date |
Mar 14, 2021 |
| Contact name |
Matt Teater |
| E-mail(s) |
mrt2001@med.cornell.edu
|
| Organization name |
Weill Cornell Medical College
|
| Street address |
445 E 69th St
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE146544 |
Acute myeloid leukemia cells resist chemotherapy through a transient senescence-like state |
| GSE146592 |
Acute myeloid leukemia cells resist chemotherapy through a transient senescence-like state [PDX] |
|
| Relations |
| BioSample |
SAMN14323093 |
| SRA |
SRX7867432 |
