|
| Status |
Public on May 01, 2024 |
| Title |
shBRD9-81-C |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Blood
cell type: CD34 HSPC
genotype: BRD9 knockdown
treatment: Lentiviral infection/FACS sort
|
| Treatment protocol |
High titer lentivirus infection was carried out at MOI 30 in presence of 10 microg/mL protamine sulphate
|
| Growth protocol |
Cells were placed in CD34 media containing IMDM+20%BIT and 100ng/mL rH-SCF and FL, and 50ng/mL TPO, supplemented with 100microM 2-mercaptoethanol and genatmicin/ciprofloxacin
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using Qiagen Rneasy kit
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
shBRD9 rep C
|
| Data processing |
Sequence reads were trimmed for adapter sequences and poor quality nucleotides using Trimmomatic v.0.36
Trimmed reads were mapped using the STAR aligner v2.5.2b
Unique gene hit counts were calculated using Subread package v.1.5.2
DESeq2
Assembly: Homo sapiens GRCh38
Supplementary files format and content: comma seperated value file contains raw counts per sample
|
| |
|
| Submission date |
Apr 15, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Swati Garg |
| E-mail(s) |
swati.garg15@gmail.com
|
| Organization name |
Dana Farber Cancer Institute
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE264008 |
BRD9 regulates normal human hematopoietic stem cell function and lineage differentiation [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN40976698 |
| SRA |
SRX24269197 |
