|
| Status |
Public on Apr 30, 2023 |
| Title |
Jurkat shTAL1 TAL1-short 2 |
| Sample type |
SRA |
| |
|
| Source name |
T-cell
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: T-cell
cell line: Jurkat
cell type: silenced endogenous TAL1 by stable transfection of inducible TAL1 shRNA targeting its 3' UTR
treatment: over expression of Short TAL gene isoform
|
| Treatment protocol |
The experiments described in this manuscript were approved by the Soroka Medical Center, Beer sheva, under IRB-SCRO protocol 0005-14-SOR. iPSCs were cultured on Matrigel-coated 6-well plates in with daily replacements of Nutristem (Biological Industries, Ltd). Cells were cultured at 37°C and 5% CO2. Cells were passaged weekly using EZ-Lift (Millipore) according to the manufacturer’s instructions.
|
| Growth protocol |
The experiments described in this manuscript were approved by the Soroka Medical Center, Beer sheva, under IRB-SCRO protocol 0005-14-SOR. iPSCs were cultured on Matrigel-coated 6-well plates in with daily replacements of Nutristem (Biological Industries, Ltd). Cells were cultured at 37°C and 5% CO2. Cells were passaged weekly using EZ-Lift (Millipore) according to the manufacturer’s instructions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA Purification kit (Norgen Biotek Corp.)
KAPA Stranded mRNA-seq Kit (Roche)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The processed reads were aligned with TopHat , allowing for 5 mismatches to the reference human genome GRCh38, with annotations from Ensembl release 106.
Quantification was done with htseq-count
Normalization, quality control plots (PCA, MA-plots) and differential expression analysis were performed using the DESeq2 package
Pair-wise comparisons were tested with default parameters using the Wald test, without using the independent filtering algorithm. Significance threshold was taken as p-adj<0.1. In addition, significant genes were further filtered by the log2(fold change) value. This filtering was baseMean-dependent and required a baseMean above 5 and an absolute log2FoldChange higher than 5/sqrt(baseMean) + 0.3.for highly expressed genes this means a requirement for a fold-change of at least 1.2, while genes with a very low expression would need a 5.8 -fold change to pass the filtering
Assembly: GRCh38, with annotations from Ensembl release 106
Supplementary files format and content: DESeq2 normalized base mean conts per gene ( ensembl gene id, Symbol) per samples
|
| |
|
| Submission date |
Oct 05, 2022 |
| Last update date |
Apr 30, 2023 |
| Contact name |
Inbar Plaschkes |
| Organization name |
HUJI
|
| Department |
The Faculty of Medicine - Ein Kerem
|
| Street address |
The Hebrew University of Jerusalem - Ein Kerem
|
| City |
Jerusalem |
| ZIP/Postal code |
91120 |
| Country |
Israel |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE214833 |
Hematopoiesis and cell growth are differentially regulated by TAL1 isoforms |
|
| Relations |
| BioSample |
SAMN31159281 |
| SRA |
SRX17803056 |
