|
| Status |
Public on Dec 04, 2014 |
| Title |
CSR-Act_B_H3K27Ac_ChIP-Seq - input |
| Sample type |
SRA |
| |
|
| Source name |
CSR activated B cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: splenic B cells actvated with antiCD40 plus IL4 at Day 2.5
strain: 129SVE(129S6)
chip antibody: input
|
| 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 |
SAMN03107028 |
| SRA |
SRX732507 |
