|
| Status |
Public on Dec 09, 2024 |
| Title |
SETD1AKO_FKBP-SETD1A_DMSO_1h_EU_30min |
| Sample type |
SRA |
| |
|
| Source name |
MOLM-13
|
| Organism |
Homo sapiens |
| Characteristics |
stimulation: DMSO
time: 1h
cell line: MOLM-13
|
| Treatment protocol |
HA-FKBP-hSETD1A expression vector, Cas9 expression vector and SETD1A sgRNA expression vector were introduced with lentivirus and stable expressing single cell clone was established. Cells were treated with DMSO or 500 nM dTAG-13 for 24 or 96 hours.
|
| Growth protocol |
MOLM-13 cells and MV4-11 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was collected using Rneasy Mini Kit with DNase (QIAGEN)
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
BCL2FASTQ version2.20.0 software was used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Aug 10, 2022 |
| Last update date |
Dec 09, 2024 |
| Contact name |
Masaki Fukuyo |
| E-mail(s) |
fukuyo@chiba-u.jp
|
| Organization name |
Chiba University
|
| Department |
Department of Molecular Oncology
|
| Street address |
1-8-1 Inohana, Chuo-ku
|
| City |
Chiba |
| ZIP/Postal code |
260-8670 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE189893 |
SETD1A regulates transcriptional pause release of heme biosynthesis genes in leukemia [RNA-seq] |
| GSE189894 |
SETD1A regulates transcriptional pause release of heme biosynthesis genes in leukemia |
|
| Relations |
| BioSample |
SAMN30242800 |
| SRA |
SRX17024200 |
