|
| Status |
Public on Nov 15, 2016 |
| Title |
HL-60 FFPE RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
HL-60 FFPE
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HL-60
cell type: acute myeloid leukemia (AML) cell line
disease state: acute myeloid leukemia (AML)
|
| Treatment protocol |
Other: Cell lines were embedded in paraffin blocks after formalin fixation (FFPE) and used as a compare/contrast control.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
AllPrep DNA/RNA FFPE Kit
Other: Total RNA from FFPE samples was extracted with the AllPrep DNA/RNA FFPE Kit (QIAGEN) according to the manufacturer's instructions.
Smear analysis of the FFPE RNA was performed on the Agilent Bioanalyzer with the Agilent RNA 6000 Nano Kit. Only samples whose RNA was not excessively degraded (DV200 >30%) were used to generate FFPE RNA-Seq libraries with the TruSeq RNA Access kit (Illumina) according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Processed data in Series supplementary file RNA-Seq_FFPE_BPDCN_Normalized.xls
|
| Data processing |
RNA-Seq Analysis (NextSeq)
Calculation Method: Pair-end sequencing was performed on a NextSeq 500 sequencer with v2 sequencing reagents (2x76bp reads). To calculate Digital Gene Expression values, the pair-end reads were aligned to hg19 genome with STAR software. The total number of reads within each gene was counted using HTSeq software. Once the total number of reads within each gene was counted, we generated for each sample the 90% trimmed mean of the read counts (average of the read counts for the middle 90% of genes in that sample). We then normalized all counts in a given sample by dividing by the samples trimmed mean and multiplying by 500. Genes with normalized counts less than 1 were set equal to one. Finally we log2 transformed the normalized counts to generate the final gene expression values.
Supplementary_files_format_and_content: Excel spread sheet of log2 transformed normalized counts
Genome_build: hg19
|
| |
|
| Submission date |
Jul 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Louis M. Staudt |
| E-mail(s) |
lstaudt@mail.nih.gov
|
| Phone |
301-402-1892
|
| Organization name |
National Cancer Institute
|
| Department |
Lymphoid Malignancies Branch
|
| Lab |
Louis M Staudt
|
| Street address |
9000 Rockville Pike, Bldg 10, Rm 4N114
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE84471 |
A Druggable TCF4- and BRD4-dependent Transcriptional Network Sustains Malignancy in Blastic Plasmacytoid Dendritic Cell Neoplasm (RNA-Seq) |
|
| Relations |
| BioSample |
SAMN05410335 |
| SRA |
SRX1951833 |
