|
| Status |
Public on Jun 04, 2020 |
| Title |
GFP_16h_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
ILC2 cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: plck-Id1 mice
tissue: thymus
transduction: GFP
time point: 16h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ATAC transposase reactions were carried out using the NX#-TDE1, TAGMENT DNA enzyme and buffer from Illumina. The reaction was purified using Qiagen miniElute columns, which is followed by PCR amplification with matching primers. The PCR products were purified using magnetic beads and eluted in EB buffer (Qiagen).
ATAC libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ILC2 cells transduced with MIGR1 vector expressing E47-ER
GFP_16h_idr.conservative_peak.narrowPeak
GFP-3_16h_S2_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval.signal.bigwig
|
| Data processing |
Raw fastq files were processed using the ENCODE-DCC ATAC-Seq Pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline). Briefly, adapters were trimmed with CutAdapt and aligned to mm10 using Bowtie2.
Aligned data were filtered for PCR duplicates, blacklisted regions, and shifted +4bp for the + strand and -5bp for the – strand.
Peaks were called using MACS2 (Zhang et al., 2008) and filtered by Irreproducible Discovery Rate (IDR < 0.1) (https://github.com/nboley/idr). Differential peak calling was performed using DiffBind (Stark R, Brown G (2011))
Signal enrichment tracks were generated with MACS2 "bdgcmp -m ppois" and represent the stastical significance of the fold enrichment of signal over expected background.
Genome_build: mm10
Supplementary_files_format_and_content: IDR peaksets in narrowPeak format; p-value signal tracks in bigWig format
|
| |
|
| Submission date |
Jun 03, 2020 |
| Last update date |
Jun 04, 2020 |
| Contact name |
Jonathan Wren |
| E-mail(s) |
Jonathan-Wren@omrf.org
|
| Phone |
(405) 271-6989
|
| Organization name |
OMRF
|
| Department |
Genes & Human Disease Research Program
|
| Street address |
825 N.E. 13th Street
|
| City |
Oklahoma City |
| State/province |
OK |
| ZIP/Postal code |
73104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE151737 |
E proteins orchestrate dynamic transcriptional cascades implicated in the suppression of the differentiation of group 2 innate lymphoid cells [ATAC-Seq] |
| GSE151739 |
E proteins orchestrate dynamic transcriptional cascades implicated in the suppression of the differentiation of group 2 innate lymphoid cells |
|
| Relations |
| BioSample |
SAMN15096287 |
| SRA |
SRX8465587 |
