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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 14, 2021 |
| Title |
293T_H3K27ac_OE |
| Sample type |
SRA |
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| Source name |
Breast cancer cells
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| Organism |
Homo sapiens |
| Characteristics |
strain: MDA-MB-231 derived LM2-4175 cells
chip antibody: H3K27ac(Abcam,ab177178)
treatment: overexpressing miR-339
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| Treatment protocol |
Transfecting miR-339 expression lentivirus into 4175 cells.
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| Growth protocol |
human breast cancer MDA-MB-231 derived LM2-4175 cells and 293T cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, HyClone) supplemented with 10% fetal calf serum (HyClone). All cells were incubated in a humidified atmosphere at 37°C in 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody for ChIP seq; Total RNA extract was harvested using Trizol reagent for RNA seq.
For ChIP-seq, libraries were prepared according to Illumina's instructions. 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 ~300 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. For RNA-seq, RNA libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: peak text files; matrix table with raw gene counts for every gene and every sample
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| Submission date |
May 06, 2021 |
| Last update date |
Sep 14, 2021 |
| Contact name |
Ying Liang |
| E-mail(s) |
16111510047@fudan.edu.cn
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| Phone |
18717906439
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| Organization name |
Fudan University
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| Street address |
Room 416, West Building 13, Dong'an Road 130, Xuhui District
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE174002 |
Reactivation of Tumor Suppressor in Breast Cancer by Enhancer Switching through NamiRNA Network |
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| Relations |
| BioSample |
SAMN19053483 |
| SRA |
SRX10809653 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5284380_OE_293T_H3K27ac_rep1.bigwig |
44.0 Mb |
(ftp)(http) |
BIGWIG |
| GSM5284380_OE_293T_H3K27ac_rep2.bigwig |
50.3 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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