|
| Status |
Public on Jun 21, 2021 |
| Title |
RNA_p4_Treated, AML |
| Sample type |
SRA |
| |
|
| Source name |
CD34+ leukemic blasts
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: AML
tissue: bone marrow
cell source: Cryopreserved patient sample
treatment: ATRA+TCP Treated cycle2 day1
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were isolated by Miltenyi CD34 microbead kit according to the manufacturer’s instructions. In brief, selection was performed immediately after defrosting the cryopreserved bone marrow patient samples. Samples were thawed in 37°C and DNase-I (Sigma D4513) was added to the samples to prevent cells clumping. Cells were resuspended in 2% FBS + IMDM medium. Cell pellets were resuspended in FcR blocking reagent and CD34 microbeads; incubated for 30 minutes. Positive selection of CD34+ cells were performed on MACS MS columns (Miltenyi Biotec 130-042-201). Cells were lysed with Trizol reagent (Invitrogen) and total RNA was extracted using miRNeasy Micro Kit (Qiagen) following manufacturer's protocol.
Preparation of total RNA for sequencing on the Illumina NovaSeq 6000 NGS platform was carried out at the University of Miami’s Hussman Institute for Human Genomics (http://hihg.med.miami.edu/cgt). Briefly, 1ng of total RNA was ribo-depleted and library construction was performed using the ‘Nugen Ovation SoLo RNA-Seq (Human) (Rev. M01406 v3) with AnyDeplete Probe Standard Human/Mouse (rRNA)’ according to manufacturer’s protocol. Samples were barcoded to allow for multiplexing. Cluster generation and sequencing took place on the Illumina NovaSeq 6000 using the reagents provided in the Illumina NovaSeq 6000 S1 Reagent Kit (200 cycle) with >60M paired-end 100 reads per sample
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Patients_treated_raw_counts_gene_expression.txt
Patients_treated_normalized_gene_expression_RPKM.txt
|
| Data processing |
RNA-seq: FASTQ data were processed with Trimmomatic v0.38 to remove adapters and low-quality reads.
RNA-seq: reads were aligned to the hg38 human genome using STAR aligner v 2.5.3a with default parameters and RSEM v1.2.28 to obtain expected gene counts against the human Ensembl (release 97).
Genome_build: hg38
Supplementary_files_format_and_content: The processed data files are in txt format : Total RNA-seq raw counts per gene and gene expression normalized by Reads Per Kilobase of transcript, per Million mapped reads (RPKM) using Deseq2.
|
| |
|
| Submission date |
Sep 29, 2020 |
| Last update date |
Jun 21, 2021 |
| Contact name |
Ramin Shiekhattar |
| Organization name |
University of Miami - Sylvester Comprehensive Cancer Center
|
| Department |
Department of Human Genetics
|
| Street address |
1501 NW 10th Avenue
|
| City |
Miami |
| State/province |
Florida |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE151594 |
Phase I Dose Escalation Study of ATRA Combined with the LSD1 inhibitor Tranylcypromine in AML and MDS |
|
| Relations |
| BioSample |
SAMN16294717 |
| SRA |
SRX9218458 |
