|
| Status |
Public on Jul 22, 2020 |
| Title |
BE2C_Flag-LIN28Bwt_yDox_input |
| Sample type |
SRA |
| |
|
| Source name |
Neuroblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BE2C
cell type: Neuroblastoma cells
|
| Treatment protocol |
Cells were treated (yDox) with doxycycline at 50 ng/ml for 3 days.
|
| Growth protocol |
The BE2C, CHP134 or Kelly neuroblastoma cells were maintained in RPMI 1640 Medium (GIBCO) supplemented with 10% fetal bovine serum (Sigma) and 1X penicillin-streptomycin (GIBCO).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and target bound fragments were isolated with antibody.
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
20180302_WTplusD-input_TT5313_S6
|
| Data processing |
ChIP-Seq reads were aligned to the hg19 revision of the human reference genome using Bowtie with parameters -k 2 -m 2 –best and -l set to the read length.
WIG files were made using MACS 1.4 with parameters -w -S –space=50 –nomodel –shiftsize=200 and subsequently normalized for the millions of mapped reads in each sample.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1
|
| |
|
| Submission date |
Oct 10, 2019 |
| Last update date |
Jul 22, 2020 |
| Contact name |
Ting Tao |
| E-mail(s) |
taot@zju.edu.cn
|
| Organization name |
Children's Hospital, Zhejiang University School of Medicine
|
| Lab |
Ting Tao
|
| Street address |
3333 Binsheng Road
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310052 |
| Country |
China |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE138742 |
LIN28B Regulates Transcription and Potentiates MYCN-induced Neuroblastoma in a let-7-independent Manner [ChIP-seq] |
| GSE138743 |
LIN28B Regulates Transcription and Potentiates MYCN-induced Neuroblastoma in a let-7-independent Manner |
|
| Relations |
| BioSample |
SAMN13015004 |
| SRA |
SRX6977277 |
