|
| Status |
Public on Jul 29, 2023 |
| Title |
sgEmpty_3 |
| Sample type |
SRA |
| |
|
| Source name |
MOLM-13;iCas9
|
| Organism |
Homo sapiens |
| Characteristics |
stimulation: Dox
time: 6d
cell line: MOLM-13
genotype: sgEmpty
|
| Treatment protocol |
Setd1afl/fl;CreER;MLL-AF9 leukemia cells were infected with retrovirus vector containing GFP or hSETD1A-GFP-CDT expression construct and then treated with tamoxifen (or EtOH as control) for 72h. Doxycycline-inducible Cas9 expression vector was introduced with lentivirus and stable expressing single cell clone was established. sgRNA vector was introduced with lentivirus and GFP-positive cells were collected by cell sorter. 1 µg / mL of Doxycycline was treated for 6 days.
|
| Growth protocol |
Mouse leukemai cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum and 10 ng/mL rmIL-3. MOLM-13 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 (Invitrogen, Carlsbad, CA)
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 |
| |
|
| Description |
SETD1A-BuGZ_RNAseq_sgBuGZ_FPKM_Hoshii20230609edited.txt
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Reads from sample no.1-16 were aligned with HISAT2.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.0.2.
Assembly: mm10 or hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Jun 15, 2023 |
| Last update date |
Jul 29, 2023 |
| Contact name |
Masaki Fukuyo |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE159145 |
SETD1A function is mediated through interaction with mitotic regulators BuGZ/BUB3 in leukemia [RNA-seq] |
| GSE159146 |
SETD1A function is mediated through interaction with mitotic regulators BuGZ/BUB3 in leukemia. |
|
| Relations |
| BioSample |
SAMN35743230 |
| SRA |
SRX20686991 |
