|
| Status |
Public on Oct 01, 2020 |
| Title |
Input-ad-ube3b-RNAPII |
| Sample type |
SRA |
| |
|
| Source name |
Raji cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: B lymphocyte
tissue: peripheral blood
morphology: lymphoblast
chip antibody: none
|
| 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.Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~150 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Illumina bcl2fq software was used for basecalling.
Low-quality reads (Q≤19 bases over 50%), Ns reads (N%>5%) and adapter polluted reads (adapter bases>5 bp) are filtered out.
ChIP-seq reads were aligned to the human genome assembly using Bowtie2.
Peaks were called using MACS2.
Genome_build: mm9
|
| |
|
| Submission date |
Feb 19, 2019 |
| Last update date |
Oct 03, 2020 |
| Contact name |
wang feng |
| E-mail(s) |
wangfeng123@imm.ac.cn
|
| Phone |
15624968856
|
| Organization name |
Chinese Academy of Medical Sciences & Peking Union Medical College,
|
| Street address |
nan wei road
|
| City |
bei jing |
| ZIP/Postal code |
associate professor |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE126258 |
TRIB3 Promotes C-Myc-Associated Lymphomagenesis through Inhibition of UBE3B-Mediated c-Myc Degradation |
| GSE126745 |
Genome-wide maps of chromatin state in ad-ube3b or Pep2-CM4-treated and control lymphoma cells |
|
| Relations |
| BioSample |
SAMN10965594 |
| SRA |
SRX5391542 |
