|
| Status |
Public on Sep 25, 2019 |
| Title |
CH12F3NCdel_aCD40_IL4_TGFb_input |
| Sample type |
SRA |
| |
|
| Source name |
CH12F3 murine lymphoma cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: AID-deficient CH12F3 murine lymphoma cells
passages: 8--10
strain: C57BL/6
chip antibody: none
treatment: with aCD40/IL4/TGFb stimulation
|
| Treatment protocol |
Purified B cells were stimulated with either aCD40/IL4 for 48 hrs; CH12F3 cell lines were cultured in lymphocyte medium R15 and stimulated with anti-CD40+IL4+TGF-β for 24 hrs.
|
| Growth protocol |
RPMI1640+10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (IP-202-1012).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Reads were aligned using bowtie2 with --non-deterministic flag
peaks were called with MACS2 with the following flags: --nomodel --keep-dup all --extsize 51 --nolambda -B --SPMR
wig files were generated using USCS utilities bedGraphToBigWig
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated for displaying
|
| |
|
| Submission date |
Apr 24, 2019 |
| Last update date |
Sep 26, 2019 |
| Contact name |
Frederick W Alt |
| E-mail(s) |
jianqiao.hu@childrens.harvard.edu
|
| Organization name |
Boston Children's Hospital
|
| Department |
PCMM
|
| Lab |
Alt
|
| Street address |
1 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE130264 |
Chromatin Loop Extrusion Plays a Fundamental Mechanistic Role in Antibody Class Switching [ChIP-Seq] |
| GSE130270 |
Chromatin Loop Extrusion Plays a Fundamental Mechanistic Role in Antibody Class Switching |
|
| Relations |
| BioSample |
SAMN11491216 |
| SRA |
SRX5730161 |
