|
| Status |
Public on Jan 30, 2023 |
| Title |
OCIAML3_NPM1c-FKBP_RNA_dTAG13_24h_REP2_200122_ACTTGA_S8 |
| Sample type |
SRA |
| |
|
| Source name |
Derivative of cell line OCI-AML3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: OCI-AML3-NPM1c-FKBP12
timepoint: 24 hours
treatment: 500nM dTAG13
|
| Treatment protocol |
Treatment regimens indicated for each sample.
|
| Growth protocol |
Human cell lines were cultured in RPMI with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA isolation, cells were lysed in 350 µl of RLT buffer and RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturers instructions.
Poly-A tail selection and library preparation were performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA).
Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) was used to obtain 1-5´107 unique sequencing paired-end tags
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human (Gencode GRCh38/hg38) using STAR (v2.7.5a, sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
RNA-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75).
Raw per-gene counts calculated with HTSeq (htseq-count, v0.6.1pl).
Differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using raw unnormalized per-gene counts from deduplicated BAMs.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: DESeq2 differential expression summary data (Excel .xlsx format)
|
| |
|
| Submission date |
Feb 10, 2022 |
| Last update date |
Jan 30, 2023 |
| Contact name |
Charlie Hatton |
| E-mail(s) |
Charles_Hatton@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Pediatric Oncology
|
| Lab |
Scott Armstrong/CPCT
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE196477 |
Mutant NPM1 binds chromatin and directly regulates oncogenic transcription in acute myeloid leukemia [RNA-seq] |
| GSE196480 |
Mutant NPM1 binds chromatin and directly regulates oncogenic transcription in acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN25829535 |
| SRA |
SRX14127327 |
