|
| Status |
Public on Nov 23, 2021 |
| Title |
Em bait_Resting splenic B cell-rep_U2 |
| Sample type |
SRA |
| |
|
| Source name |
Resting splenic B cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Resting splenic B cells
treatment: unstimulated
|
| Treatment protocol |
Cells were crosslinked using 1% formaldehyde. Hind III and DpnII were used as the primary and secondary restriction enzymes, respectively for each of two biological replicates. Inverse PCR was performed using the Expand Long Template PCR System from two viewpoints with barcoded primers
|
| Growth protocol |
Resting splenic B cells were sorted for CD43- resting B cells using anti-CD43 magnetic microbeads (MACS, Miltenyi) according to the manufacturer’s instructions. B cells cultured at a density of 5-8 x 105 cells/ml in RPMI, glutamine (4 mM), penicillin (100 U/ml)-streptomycin (100 mg/ml), b-mercaptoenthanol (50 mM), supplemented with FCS (20% vol/vol) with the activators, LPS (50 mg/ml) and IL4 (10 ng/ml). Rag2-/- pro-B cells that were cultured with IL7 and expanded in ex vivo culture for 4-5 days. Splenic T cells that were enriched using the mouse T cell enrichment column kit (MTCC-5, R&D) and cultured with ConA (5ng/ml) (15324505, MP Biomedical).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
* The library was quantitated by qPCR and sequenced on one lane for 101 cycles on a HiSeq2000 using a TruSeq SBS sequencing kit version 3 and analyzed with Casava1.8.2. PhiX library was spiked into the lane at approximately 10% to balance the imaging cycles for higher quality.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Em-bait
|
| Data processing |
Library strategy: 4C-seq
Reads were trimmed and aligned to an in silico library constructed based on the mouse (Mus musculus) genome (mm9)
The quality-scores line in fastq files processed with Casava1.8 use an ASCII offset of 33 (known as Sanger scores) instead of the previous 64 offset
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated
|
| |
|
| Submission date |
Aug 29, 2021 |
| Last update date |
Nov 23, 2021 |
| Contact name |
Amy Kenter |
| E-mail(s) |
star1@uic.edu
|
| Organization name |
University of Illinois at Chicago
|
| Street address |
835 S Wolcott Ave
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60612 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE183006 |
4C-seq analyses of the 3’Igh locus during B cell development |
|
| Relations |
| BioSample |
SAMN21032587 |
| SRA |
SRX11960782 |
