|
| Status |
Public on Dec 22, 2021 |
| Title |
ATAC-Seq NoDox_IRF4_Runx3_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
NIH/3T3 Fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
sample group: Ectopic_Expression_In_Fibroblasts
replicate group: NoDox_IRF4_Runx3
timepoint: NA
condition: Please see the fibroblast columns for details.
primary stimulation: NA
restimulation: NA
dox_added_to_fibroblast: No
batf_expressed_in_fibroblast: No
irf4_expressed_in_fibroblast: Yes
tbet_expressed_in_fibroblast: No
runx3_expressed_in_fibroblast: Yes
|
| Treatment protocol |
In vitro P14 CD8+ T cells: on day 6, cells were left untreated or activated with 50 ng/ml PMA and 1 uM ionomycin for 3 hours before harvest for ATAC-seq. In vivo P14 CD8+ T cells: no treatment. NIH/3T3 fibroblast: cells were transduced with doxycycline-inducible TF-expressing lentivirus. Fibroblasts were left untreated or treated with 4 ug/ml doxycline for 72 hours for TFs induction before harvest for ATAC-seq.
|
| Growth protocol |
In vitro P14 CD8+ T cells: naïve CD8+ T cells were isolated with Miltenyi kit (Cat#130-096-543), stimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI (supplemented with HEPES, NEAA, sodium pyruvate, 2-Mercaptoethanol, 10% FBS) in the presenece of 100 U/ml IL-2. In vivo P14 CD8+ T cells were sorted directly from LCMV infected mice. NIH/3T3 fibroblast: cells were cultured in DMEM supplemented with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell nuclei were extracted and proceed directly to the Tn5 transposition reaction and library preparation.
Briefly, Tn5 transposase (Illumina #FC-121-1030) was used for genomic DNA fragmentation and the transposed DNA fragments were PCR amplified and barcoded with Illumina Nextera Index Kit (FC-121-1011).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
NoDox_IRF4_Runx3_Rep1
|
| Data processing |
ATAC-seq reads were trimmed using Trimmomatic to remove primer and low-quality bases.
The paired-end reads were then aligned to the mm10 reference genome using bowtie2, allowing maximum insert sizes of 2000 bp, with the “--no-mixed” and “--no-discordant” parameters added.
Reads with a mapping quality (MAPQ) below 30 were removed.
Duplicates were removed with PicardTools, and the reads mapping to the blacklist regions and mitochondrial DNA were also removed.
Reads mapping to the positive strand were moved +4 bp, and reads mapping to the negative strand were moved -5bp following the procedure outlined by Buenrostro et al. to account for the binding of the Tn5 transposase.
Peaks were called using macs2 qith a qvalue of 0.001.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited files of peaks identified with macs2 using a qvalue of 0.001
|
| |
|
| Submission date |
Dec 21, 2021 |
| Last update date |
Dec 22, 2021 |
| Contact name |
Jim Kaminski |
| E-mail(s) |
[email protected]
|
| Organization name |
Boston Children's Hospital
|
| Street address |
1 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE192385 |
Batf-mediated Epigenetic Control of Effector CD8+ T Cell Differentiation (ATAC-Seq) |
| GSE192390 |
Batf-mediated Epigenetic Control of Effector CD8+ T Cell Differentiation |
|
| Relations |
| BioSample |
SAMN24281708 |
| SRA |
SRX13473785 |
