|
| Status |
Public on Aug 10, 2022 |
| Title |
0 hour |
| Sample type |
SRA |
| |
|
| Source name |
SK-N-BE2 Neuroblastoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SK-N-BE2 Neuroblastoma cell line
time point: Hour 0
treatment: 21% oxygen
genotype: WT
|
| Treatment protocol |
normoxia (21% O2) vs hypoxia (1% O2)
|
| Growth protocol |
SK-N-BE(2) neuroblastoma cell line cultured in RPMI with 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was from cell pellets were sheared to 300bp. 5-hmC was labeled with UDP-6'-azide-glucose by T4 glucosyltransferase, then biotin-S-S-DBCO via Click reaction. 5-hmC containing DNA fragments were then captured using streptavidin beads, washed, released from beads by DTT cleavage of S-S bond, and purified for sequencing
Library was prepared with standard Illumina protocol by the University of Chicago Sequencing Core
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Library strategy: hMe-SEAL
fastq reads were aligned to hg19 reference genome with BWA/0.7.17
Peaks were called by MACS2 for each sample using input as control
Numbers of reads in each peak quantified by Htseq-count
Counts normalized to FPKM
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files containing peak positions and calculated FPKM value of each peak
|
| |
|
| Submission date |
Feb 24, 2021 |
| Last update date |
Aug 11, 2022 |
| Contact name |
Anastasia Hains |
| E-mail(s) |
hainsa@uchicago.edu, hains@stanford.edu
|
| Phone |
4149752475
|
| Organization name |
Stanford University
|
| Street address |
269 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE167475 |
MYCN directly regulates TET1 expression to control 5-hmC distribution and enhance neuroblastoma cell migration in hypoxia [hMe-SEAL] |
| GSE167478 |
MYCN directly regulates TET1 expression to control 5-hmC distribution and enhance neuroblastoma cell migration in hypoxia |
|
| Relations |
| BioSample |
SAMN18053272 |
| SRA |
SRX10165706 |
