|
| Status |
Public on Jul 08, 2024 |
| Title |
CD4_mem_sgNT_AHR_CnR_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
primary CD4+ memory T cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary CD4+ memory T cells
treatment: Non-targeting guide, AHR agonist (TCDD)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT&RUN was performed using the CUTANA ChIC / CUT&RUN Kit (EpiCypher #14-1048) and following manufacture protocol with minor modifications.
CUT&RUN library prep was performed using KAPA HyperPrep Kit (Roche)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
nt2
|
| Data processing |
All libraries were proccessed with using a pipeline with script adapted and modified from the following repository: https://github.com/wherrylab/jogiles_ATAC. The pipeline assess FASTQ files using FASTQC, reads were aligned to GRCh38 using Bowtie 2. Samtools was used to remove unmapped, unpaired and mitochondrial reads and ENCODE blacklist regions. PCR duplicates were removed uisng Picard.
We used SEACR with 'relaxed' peak selection mode to call target peaks over IgG control therefore no peaks files for IgG. Number of reads in each peak was determined using BedTools coverage. Peak annotation was done using ChIPseeker package in R.
Differentially bound peaks were identified using Diffbind package in R, following DESeq2 normalization using FDR cut-off of 0.05 unless otherwise indicated.
Motif enrichment analysis was performed using HOMER.
Tracks were visualized using Integrative Genomics Viewer.
Assembly: hg38
Supplementary files format and content: bigwig, for graph viewing on integrative genomics viewer.
Supplementary files format and content: bed, called peaks.
Supplementary files format and content: csv, Diffbind normalized counts.
Library strategy: CUT&RUN
|
| |
|
| Submission date |
May 21, 2023 |
| Last update date |
Jul 08, 2024 |
| Contact name |
Calvin Law |
| E-mail(s) |
calvin.law@northwestern.edu
|
| Organization name |
Northwestern University
|
| Department |
Dermatology
|
| Lab |
Choi Lab
|
| Street address |
303 E Superior St Lurie 5-220
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE233045 |
Interferon subverts an AHR-JUN axis to promote CXCL13+ T cells in lupus [AHR] |
| GSE233050 |
Interferon subverts an AHR-JUN axis to promote CXCL13+ T cells in lupus |
|
| Relations |
| BioSample |
SAMN35298802 |
| SRA |
SRX20460990 |
