|
| Status |
Public on Sep 15, 2022 |
| Title |
scRNAseq_BT869_SMARCA4ko_d4_rep1_cell159 |
| Sample type |
SRA |
| |
|
| Source name |
BT869
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BT869
cell type: H3.3K27M-glioma
genotype: SMARCA4 knockout
treatment: nucleofection
time: 4 days
|
| Growth protocol |
BT869 cells were grown as neurospheres in tumor stem media base supplemented with B27 minus vitamin A (Thermo Fisher Scientific), human growth factors (EGF, FGF, PDGF-AA, PDGF-BB [Shenandoah Biotechnology]) and heparin (Stemcell Technologies) in ultra-low attachment flasks in humidified atmosphere with 5% CO2 at 37C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Live cells were FACS sorted into 96-well plates containing TCL lysis buffer (Qiagen) and plates were frozen prior to processing for Smart-seq2
SMART-seq2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
SMART-seq2
D4SM4R1-P2-F03
|
| Data processing |
Raw sequencing reads were aligned by bowtie, and gene counts were quantified using RSEM as transcript-per-million, or TPM.
Expression levels were calculated as Ei,j = log2(TPMi,j/10 + 1) for gene i in sample j. TPM values were divided by 10 for better approximation of the estimated complexity of single-cell libraries.
We filtered out low quality cells with less than 2,500 detected genes or an average housekeeping expression level below 2.5 and removed low expressed genes with TPM greater than 16 in less than 5 cells.
We defined relative expression as centered expression levels, Eri,j = Ei,j − average[Ei,1...n] for the remaining cells and genes.
Assembly: hg19
Supplementary files format and content: TPM values for each gene in each cell and in every condition. Control AAVS1 (CTRL) and SMARCA4 knockout (SM4KO) TPM data are gathered in one csv file per replicate.
|
| |
|
| Submission date |
Sep 06, 2022 |
| Last update date |
Sep 15, 2022 |
| Contact name |
Joana Graca Marques |
| E-mail(s) |
joanagracamarques@gmail.com
|
| Phone |
8572506823
|
| Organization name |
Dana-Farber Cancer Institute
|
| Street address |
360 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE212782 |
BAF complex maintains glioma stem cells in pediatric H3K27M-glioma [scRNA-seq] |
| GSE212786 |
BAF complex maintains glioma stem cells in pediatric H3K27M-glioma |
|
| Relations |
| BioSample |
SAMN30691203 |
| SRA |
SRX17453261 |
