|
Status |
Public on Dec 04, 2014 |
Title |
GCt_B_H3K27Ac_ChIP-Seq |
Sample type |
SRA |
|
|
Source name |
GC B cells
|
Organism |
Mus musculus |
Characteristics |
cell type: Germinal Center B cells purified from spleen strain: 129SVE(129S6) chip antibody: H3K27Ac (abcam, ab4729)
|
Growth protocol |
Splenic naïve B cells were purified via an αCD43/αCD11c/αGL7 negative selection approach. The purified naïve B cells were further activated with αCD40 plus IL4 for 60 hours to generate CSR-activated B cells. The VHB1-8 or WT mice were immunized with sheep red blood cells (SRBCs) for 9 days. Splenic GC B cells were purified from immunized spleens via an αCD43/αCD11c/αIgD negative selection.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
ChIP-Seq: Cell Lysates were sonicated and histone-DNA complexes were isolated with anti H3K27Ac antibody. ChIP-Seq: Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Preparation Kit. The libraries were sequenced on Illumina HiSeq2500.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
Each raw file corresponds to one biological replicate.
|
Data processing |
GRO-Seq and ChIP-Seq data sets were aligned using Bowtie software to mouse genome build mm9/NCBI37 or human genome build hg19/NCBI37. We used Homer software to de novo identify transcripts from both strands of the genome in the context of the GRO-Seq data, and considered broad sense/antisense overlap regions (>100bp) as ConvT regions. We used the MACS1.4 software to identify regions of ChIP-Seq enrichment over background with a P value threshold of 10−5. We used ROSE software to identify SEs. Genome_build: mm9 Supplementary_files_format_and_content: BigWig files were generated by using MACS2 and bedGraphtoBigWig tools.
|
|
|
Submission date |
Oct 14, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Feilong Meng |
E-mail(s) |
feilong.meng@childrens.harvard.edu
|
Organization name |
Boston Children's Hospital
|
Department |
PCMM
|
Lab |
Fredrick W Alt Lab
|
Street address |
300 Longwood Ave
|
City |
Boston |
State/province |
MA |
ZIP/Postal code |
02115 |
Country |
USA |
|
|
Platform ID |
GPL17021 |
Series (1) |
GSE62296 |
Convergent Sense/Antisense Transcription At Intragenic Super-Enhancers Targets AID-initiated Genomic Instability |
|
Relations |
BioSample |
SAMN03107027 |
SRA |
SRX732348 |
Named Annotation |
GSM1524925_H3K27ac_GCB.bw |