|
| Status |
Public on Jun 23, 2020 |
| Title |
SKOG-Input |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic cell infection with retrovirus SKO+Glis1
|
| Organism |
Mus musculus |
| Characteristics |
strain: ICR
tissue: mouse embryonic fibroblast cell
age: day 8 in reprogramming process
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 accompanying the DNA Sample Kit (Part# 0801-0303). 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 ~250 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 Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
The sequencing reads were filtered by Trimmomatic (0.35), and then mapped to mouse reference sequence for mm10 using Bowtie2 (2.2.5).
Uniquely mapped reads were retained using Samtools (1.3.1) with parameters "-F 1804 -f 2 -q 30" and Picard tools MarkDuplicates (1.90)
peaks were called using MACS2 (2.1.0) callpeak module with parameters "-p 0.01 --nomodel --extsize 150 -B --SPMR --keep-dup all --call-summits" on ChIP-seq data, and then only peaks with qvalue less than 1e-05 were keeped
Genome_build: mm10
Supplementary_files_format_and_content: Tracks of signal were computed using MACS2 bdgcmp module with parameter "-m ppois".The signal BigWig files were visualized using computeMatrix, plotHeatmap and plotProfile module in DeepTools (2.4.2)
|
| |
|
| Submission date |
May 17, 2019 |
| Last update date |
Jun 26, 2020 |
| Contact name |
LI LINPENG |
| E-mail(s) |
568638721@qq.com
|
| Organization name |
GIBH
|
| Street address |
KAIYUAN ROAD 190
|
| City |
Guangzhou |
| ZIP/Postal code |
510000 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE131426 |
Glis1 Activate Glycolytic Process and Increase H3K27Ac Level on Pluripotent and Second Wave Genes Promoter Facilitating Pluripotency Induction [ChIP-Seq] |
| GSE131692 |
Glis1 Activate Glycolytic Process and Increase H3K27Ac Level on Pluripotent and Second Wave Genes Promoter Facilitating Pluripotency Induction |
|
| Relations |
| BioSample |
SAMN11672423 |
| SRA |
SRX5858836 |
