|
| Status |
Public on Jan 17, 2024 |
| Title |
KO-PAX5 ChIP-seq_rep_1 |
| Sample type |
SRA |
| |
|
| Source name |
H1155 cell line konck out PAX5
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: neuroendocrine large cell lung cancer
genotype/variation: KO-PAX5
chip antibody: anti-H3K9me3 (ab8898,abcam), spike-in antibody (61686, Activemotif)
treatment: untreatment
|
| Treatment protocol |
untreatment
|
| Growth protocol |
H1155 and KO-PAX5 cell line were cultred in DMEM medium containg 10%FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and H3K9me3-DNA complexes were isolated with H3K9me3 antibody.
Libraries were prepared according to Illumina's instructions accompanying the Paired-End DNA Samples Prep Kit. Briefly, DNA fragment end repair, add A base to 3'end, and connect sequencing adapter. PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp 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 2500 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
KO-PAX5 ChIP-seq_rep_1
|
| Data processing |
Basecalls performed using CASAVA version 1.4
Data were filtered using Trimmomatic
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2-2.3.5
Determination of the normalized factor using deeptools
peaks were called using MACS2
Genome_build: hg38 and dm6
|
| |
|
| Submission date |
Jan 18, 2021 |
| Last update date |
Jan 17, 2024 |
| Contact name |
Yan Xue miao |
| E-mail(s) |
yanxuemiao1991@126.com
|
| Phone |
86+18630809452
|
| Organization name |
Tianjin Medical University
|
| Department |
Department of Immunologyc
|
| Lab |
Zhe Liu
|
| Street address |
22 Qixiangtai Road,Heping District,Tianjin,China
|
| City |
Tianjin |
| State/province |
Tianjin |
| ZIP/Postal code |
300070 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE165035 |
PAX5 promotes heterocharomatin formation |
|
| Relations |
| BioSample |
SAMN17373900 |
| SRA |
SRX9891017 |
