|
| Status |
Public on Sep 23, 2019 |
| Title |
H3K27me3_KD_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: SC-130356 (Santa Cruz Biotechnology)
cell line: HEK293T
cggbp1 status: knockdown
|
| Treatment protocol |
HEK293T cells were transduced with following shRNA lentiviruses: non-targeting (CT), CGGBP1-silencing (KD) and CGGBP1-overexpressing (OE). For stable transduction, control and CGGBP1 shmiR transduced cells were selected with 10 ug/ml puromycin.
|
| Growth protocol |
HEK293T cells were grown in DMEM supplemented with 10 % FBS at 37C and 5%CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclear lysates and protein-DNA complexes were isolated using specific antibodies.
The Ion Xpress(TM) Plus Fragment Library Kit (Cat. no. 4471269) was used for library preparation. All the steps were performed as per manufacturer’s instructions for sequencing on Ion Torrent S5 platform without any barcoding.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Ion Torrent S5 |
| |
|
| Description |
H3K27me3_KD_peaks.bed pvalue = p<0.001
|
| Data processing |
Filtering: Unpaired sequencing reads were trimmed and subjected to proprietary quality filtration for the Ion Torrent platform (minimum quality threshold 20). Reads with sequence length ranging from 80 to 300 base were used for further analysis.
Alignment: Reads were mapped using bowtie2 against repeat-masked (hg38.fa.masked) and repeat-unmasked (hg38.fa) human genome. Reads were mapped end-to-end with default option.
RM Filtering: Reads were mapped to repeat-masked genome. All reads with ambiguous nucleotide (N) were removed and subjected to peak-calling to get RM CTCF peaks.
Peak calling: MACS2 (single sample peak calling).
Genome_build: hg38
Supplementary_files_format_and_content: bed files with MACS2 called peaks (*peaks.bed) on sample records or overlapping peaks from different conditions made by bedtools intersect -v found on series record.
|
| |
|
| Submission date |
Apr 09, 2019 |
| Last update date |
Sep 25, 2019 |
| Contact name |
Umashankar Singh |
| Organization name |
IIT Gandhinagar
|
| Department |
Biological Sciences and Engineering
|
| Lab |
HoMeCell Lab
|
| Street address |
Acad Block 4 Room 317 IIT Gandhinagar Palaj
|
| City |
Gandhinagar |
| State/province |
Gujarat |
| ZIP/Postal code |
382055 |
| Country |
India |
| |
|
| Platform ID |
GPL23934 |
| Series (1) |
| GSE129548 |
CGGBP1 regulates chromatin barrier activity and CTCF occupancy at repeats |
|
| Relations |
| BioSample |
SAMN11375104 |
| SRA |
SRX5659188 |
