|
| Status |
Public on Jul 27, 2022 |
| Title |
EBF4 sgRNA RNA-seq rep3 [s14_3] |
| Sample type |
SRA |
| |
|
| Source name |
Jurkat T cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Jurkat T cell
treatment: EBF4 sgRNA
|
| Treatment protocol |
The lentiviral EBF4 plasmid was generated from pLV-EF1a-IRES-Puro (Addgene) vector by replacing the puromycin fragment with a truncated EGFR protein. The lentiviral EBF4 plasmid and plasmids containing PAX2 and VSV-G (Addgene) were transfected into 293T cells using Lipofectamine 3000 reagent (Invitrogen). EBF4 knockout plasmid was generated from the lentiCRISPRv2 vector (Addgene). Knockout plasmids and plasmids containing PAX2 and VSV-G (Addgene) were transfected into 293T cells using Lipofectamine 3000 reagent (Invitrogen). The culture supernatants containing lentivirus were harvested. Cell lines were seeded in complete medium supplemented with Polybrene (Sigma) and lentiviruses.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from un-stimulated Jurkat T cells was extracted and were used to prepare RNA-seq libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
s14_3
|
| Data processing |
RNA-seq data was processed using the Pipeliner workflow (https://github.com/CCBR/Pipeliner). Reads were trimmed using Cutadapt v1.18 and aligned to the human hg38 reference genome and Gencode release28 using two-pass STAR v2.7.0f. RSEM v1.3.0 was used for gene-level expression quantification, and limma v 3.38.3 was used for voom quantile normalization and differential expression analysis.
Assembly: hg38
|
| |
|
| Submission date |
Jun 15, 2022 |
| Last update date |
Sep 20, 2022 |
| Contact name |
Michael Lenardo |
| E-mail(s) |
MLENARDO@niaid.nih.gov
|
| Organization name |
NIH
|
| Department |
NIAID
|
| Street address |
9000 Rockville Pike, 10/11D14
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE206221 |
Early B Cell Factor 4 modulates FAS-mediated apoptosis and promotes cytotoxic function in human immune cells [RNA-seq] |
| GSE206222 |
Early B Cell Factor 4 modulates FAS-mediated apoptosis and promotes cytotoxic function in human immune cells. |
|
| Relations |
| BioSample |
SAMN29124527 |
| SRA |
SRX15715097 |
