|
| Status |
Public on Dec 04, 2014 |
| Title |
CSR-Act_B_GRO-Seq |
| 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)
|
| 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 |
total RNA |
| Extraction protocol |
GRO-Seq: BrU labelled nascent transcripts were extracted with Tripure reagent and affinity purified with anti-BrU antibody conjugated agarose beads.
GRO-Seq: BrU labelled nascent RNA transcripts were fragmented with NaOH, and RNA was decapped with Tobacco Acid Pyrophosphatase (TAP) and end-repaired with T4 polynucleotide kinase. Illumina Adapters were ligated to the RNA with T4 RNA ligase and cDNA was generated with Reverse Transcriptase. The libraries were PCR amplified with Illumina primers and subjected to Illumina Hiseq2000 or HiSeq2500.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Nascent RNA
Each raw file corresponds to one biological replicate.
|
| Data processing |
Library strategy: Gro-Seq
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 |
GPL13112 |
| Series (1) |
| GSE62296 |
Convergent Sense/Antisense Transcription At Intragenic Super-Enhancers Targets AID-initiated Genomic Instability |
|
| Relations |
| BioSample |
SAMN03107023 |
| SRA |
SRX732344 |
| Named Annotation |
GSM1524921_AID_iABC_merge.negative.bw |
| Named Annotation |
GSM1524921_AID_iABC_merge.positive.bw |
