|
| Status |
Public on Aug 01, 2022 |
| Title |
rep 3 AID ChIP |
| Sample type |
SRA |
| |
|
| Source name |
total (CD20+) B cells_AID ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: donors undergoing routine tonsilectomy
donor id: donor 3
tissue: tonsil
cell type: Primary Human B cells
chip antibody: AID (Abcam, ab5197)
|
| Treatment protocol |
After 48hours B cells were crosslinked and nuclei collected
|
| Growth protocol |
Primary Human B cells were isolated from the tonsils of donors undergoing routine tonsilectomy and culture in the presence of anti-CD40 antibody and rhIL-4 for 48 hours
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from Micrococcal treated and sonicated nuclei and histone-DNA complexes isolated with an antibody.
Libraries were prepared according to Illumina's instructions accompanying the CHIP-Seq sample prep kit. Libraries were sequenced on the Genome Analyzer II or HiSEq2000 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome build using Bowtie2 (Galaxy)
PCR duplicates, non-uniquely mapped sequences and prro quality reads were removed
peaks were called using MACS and SICER peak callers (Galaxy)
Following peak calling, regions with >2x average input read depth were removed. Peaks falling in known blacklisted regions (Duke blacklist) and regions of high input depth (top 0.1 of genome - UCSC) were excluded. Only peaks >4.5 fold enriched (3 fold for SICER) were used in subsequent analyses
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated by MACS
|
| |
|
| Submission date |
Oct 13, 2015 |
| Last update date |
Aug 01, 2022 |
| Contact name |
David Jonathan Fear |
| E-mail(s) |
david.fear@kcl.ac.uk
|
| Phone |
+44(0)2071880613
|
| Organization name |
Kings College London
|
| Department |
Respiratory Medicine and Allergy
|
| Street address |
5th Floor, Tower Wing, Great Maze Pond
|
| City |
London |
| ZIP/Postal code |
SE1 9RT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE73933 |
ChIP-seq Analysis of Activation-Induced Cytidine Deaminase Distribution in Human B Cells: Insights for Targeting Mechanisms |
|
| Relations |
| BioSample |
SAMN04160440 |
| SRA |
SRX1331091 |
