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Status |
Public on Aug 01, 2022 |
Title |
rep 1 Input |
Sample type |
SRA |
|
|
Source name |
total (CD20+) B cells_input
|
Organism |
Homo sapiens |
Characteristics |
subject status: donors undergoing routine tonsilectomy donor id: donor 1 tissue: tonsil cell type: Primary Human B cells
|
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.
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|
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
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
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|
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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 |
GPL11154 |
Series (1) |
GSE73933 |
ChIP-seq Analysis of Activation-Induced Cytidine Deaminase Distribution in Human B Cells: Insights for Targeting Mechanisms |
|
Relations |
BioSample |
SAMN04160435 |
SRA |
SRX1331086 |