|
| Status |
Public on Jul 27, 2022 |
| Title |
Empty vector ATAC-seq rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Jurkat T cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Jurkat T cell
treatment: empty vector
|
| 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).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We followed the Omni-ATAC protocol. Briefly, 50000 cells were washed and lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin for 10 min on ice to prepare the nuclei. Immediately after lysis, nuclei were spun at 500 x g for 10 min to remove the supernatant. Nuclei were then incubated with Tn5 transposon and tagmentation buffer (20 mM Tris-HCl (pH 7.6), 10 mM MgCl2, 20% Dimethylformamide) containing 0.1% Tween-20 and 0.005% Digitonin at 37 °C for 30 min. Stop buffer was added directly into the reaction to end tagmentation.
PCR was performed to amplify the library. Libraries were then purified with SPRI (Beckman) beads and deep sequencing was performed.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
EVp1
|
| Data processing |
Samples were trimmed for adapters using Cutadapt v 1.18 before alignment. The trimmed reads were aligned to the hg38 reference using Bowtie2 v2.3.4.1 with flag -k 10.
The peaks were called using Genrich v0.6 (https://github.com/jsh58/Genrich) with the following flags -j -y -r -v -d 150 -m 5 -e chrM,chrY. Genrich-produced bedgraphs were normalized by library size (reads per million sequenced reads, RPM) for visualization.
Assembly: hg38
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak
|
| |
|
| 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 |
GPL11154 |
| Series (2) |
| GSE206220 |
Early B Cell Factor 4 modulates FAS-mediated apoptosis and promotes cytotoxic function in human immune cells [ATAC-seq] |
| GSE206222 |
Early B Cell Factor 4 modulates FAS-mediated apoptosis and promotes cytotoxic function in human immune cells. |
|
| Relations |
| BioSample |
SAMN29124560 |
| SRA |
SRX15715811 |
