|
| Status |
Public on Nov 17, 2016 |
| Title |
ChIP-Seq-SH-SY5Y-H3K4me3 EPOP-OE |
| Sample type |
SRA |
| |
|
| Source name |
SH-SY5Y
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: EPOP Overexpression
chip antibody: H3K4me3; Millipore, #04-745
|
| Treatment protocol |
For ChIP cells were crosslinked with 1% formaldehyd for 10 min and sonicated to 200 bps.
|
| Growth protocol |
E14 mouse ES cells (ES-E14TG2a) were cultured in DMEM, 15% FCS, 1 x L-Glutamine (Invitrogen), 1 x Non-essential amino acids (Invitrogen), 1 x Penicillin/Streptomycin (Invitrogen) and LIF (Millipore) on gelatin-coated plates, SH-SY5Y cells were cultured in DMEM, 10% FCS, 1 x Penicillin/Streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA were extracted using antibodies for EPOP, H3K4me3, Elongin B, RNA Polymerase II S5, USP7 or H2Bub. RNA-Seq samples were prepared by isolating total RNA using Trizol, mRNA Isolation, heat fractionation, reverse transcription and second strand synthesis
Libraries were constructed of 10-50 ng of DNA following Illumina’s® protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
ChIP-Seq data were aligned to mouse genome mm9 or human genome hg19 using bowtie 1.0 with n = 1 and m = 3
Bigwig files were created using Galaxy/deepTools, duplicated tags were ignored
RNA-Seq data were aligned by Tophat v0.9 to mm10, using the Galaxy Platform. Normalized Values were derived using Cuffdiff v2.2.1 using a gffread filtered gencode.vM6.basic.annotation.gtf file as template
Supplementary_files_format_and_content: bigwig, txt
|
| |
|
| Submission date |
Jan 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert Liefke |
| E-mail(s) |
robert.liefke@imt.uni-marburg.de
|
| Organization name |
Philipps University of Marburg
|
| Department |
Institute of Molecular Biology and Tumor Research (IMT)
|
| Street address |
Hans-Meerwein-Str. 2
|
| City |
Marburg |
| State/province |
Hessen |
| ZIP/Postal code |
35043 |
| Country |
Germany |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE76536 |
EPOP interacts with Elongin BC and USP7 to modulate the chromatin landscape (EPOP KO) |
| GSE90045 |
EPOP interacts with Elongin BC and USP7 to modulate the chromatin landscape |
|
| Relations |
| BioSample |
SAMN04384496 |
| SRA |
SRX1517398 |
