|
| Status |
Public on Jul 31, 2024 |
| Title |
MOLM13, 5uM DB2115, 12hr PRO-seq rep2 |
| Sample type |
SRA |
| |
|
| Source name |
hematopoietic
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: hematopoietic
cell line: MOLM13
cell type: Acute myeloid leukemia
treatment: 5uM DB2115
molecule type: Nascent RNA
|
| Treatment protocol |
Cells were maintained at 1mill/ml before treatment with 5uM DB2115, or Vehicle (0.001% DMSO) for 1-12hrs
|
| Growth protocol |
Cells were maintained in 10% FBS, 1% Pen Strep, RPMI media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PRO-seq was performed in two biological replicates as previously described using approximately 20 million nuclei per run on with GTP, ATP, UTP, and biotin-11-CTP (PerkinElmer) using 0.5% Sarkosyl (Fisher Scientific) to prevent transcription initiation.
RNA was reversed transcribed and amplified to make the cDNA library for sequencing by the Vanderbilt University Medical Center (VUMC) VANTAGE Genome Sciences Shared Resource on an Illumina NovaSeq 6000 (PE-150, 50 million reads).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
MOLM13 12hr DB
|
| Data processing |
library strategy: PRO-seq
Cleaned and trimmed reads were analyzed by FastQC for base sequence quality, GC content, N content, and sequence duplication levels.
Sequencing reads passing quality control criteria were aligned to the Homo Sapiens transcriptome (hg38) using bowtie2 aligner
Nascent RNA Sequencing Analysis Pipeline was used to determine gene body changes of transcription
Assembly: hg38
Supplementary files format and content: bedgraph of positive and negative sense RNA nascent transcripts
|
| |
|
| Submission date |
May 14, 2024 |
| Last update date |
Jul 31, 2024 |
| Contact name |
Samuel John Taylor |
| E-mail(s) |
samueljtaylor89@gmail.com
|
| Organization name |
Albert Einstein College of Medicine
|
| Street address |
1300 Morris Park Ave, Chanin building 601
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE267386 |
Pharmacological Repositioning of the transcription factor PU.1 [PRO-seq] |
| GSE267389 |
Pharmacological Repositioning of the transcription factor PU.1 |
|
| Relations |
| BioSample |
SAMN41390429 |
| SRA |
SRX24542789 |
