|
| Status |
Public on Oct 01, 2020 |
| Title |
CnR_Igg_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
CD8 T cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: CD8 T cells
background strain: C57BL/6
genotype: Igg control
treatment: LCMV Clone13 infection
antibody: guinea pig anti-rabbit IgG, ABIN101961
protocol: Cut and Run Chipseq
|
| Treatment protocol |
The antibodies used were: Fli1, ab15289, used at 1:50 (abcam) and guinea pig anti-rabbit IgG, used at 1:100, ABIN101961 (antibodies-online).
|
| Growth protocol |
At D8 p.i. with Cl13, CD8 T cells were isolated from spleens of infected recipients
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT&RUN experiments were performed as previously described(Skene et al., 2018) with modifications
CUT&RUN DNA library was prepared as previously descried(Liu et al., 2018) with slight modifications. Briefly, all DNA precipitated from pA-MN digestion was used for library preparation using NEBNext Ultra II DNA Library Prep Kit (NEB).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
Igg_rep3
|
| Data processing |
Reads were aligned to mm10 reference genome using Bowtie2 v2.3.4.1 with options suggested by Henikoff (Skene et al., 2018).
Picard tools v1.96 was used to remove presumed PCR duplicates using the MarkDuplicates command. Bam files containing uniquely mapped reads were created using Samtools v1.1. For downstream analysis, biological replicates (3 per condition) were merged at this step. Bedtools v2.28.0 was used to generate fragment BED files with size 40bp-500bp. Blacklist regions, random chromosomes, and mitochondria were removed
Read per million (RPM) normalized bigwig files were created using bedGraphToBigWig (UCSC) and were used to visualize binding signals. Peaks were called using MACS v2.1 using the broadPeak setting with p-value cutoff of 1e-8, -f BEDPE and IgG as controls
Genes proximal to peaks were annotated against the mm10 genome using annotatePeaks.pl from HOMER v4. Fli1 binding motifs were identified using findMotifsGenome.pl from HOMER v4
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text file with normalized counts
|
| |
|
| Submission date |
May 04, 2020 |
| Last update date |
Oct 01, 2020 |
| Contact name |
E JOHN WHERRY |
| Organization name |
University of Pennsylvania
|
| Department |
Systems Pharmacology and Translational Therapeutics,Institute for Immunology
|
| Street address |
421 Curie Blvd,354 BRB II/III
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE149837 |
Cut and Run chipseq of Fli1 in CD8 post Cl13 infection |
| GSE149839 |
Fli1 as transcriptional safeguard that restrains effector CD8 T cell differentiation |
|
| Relations |
| BioSample |
SAMN14829304 |
| SRA |
SRX8245980 |
