|
| Status |
Public on Nov 15, 2016 |
| Title |
ChIP FLI1 |
| Sample type |
SRA |
| |
|
| Source name |
Kasumi-1_ChIP-seq
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Kasumi-1
cell type: human acute myeloid leukemia cell line
antibody target: FLI1
chip antibody vendor: Santa cruz
chip antibody cat. #: sc-356
|
| Treatment protocol |
shRNA was induced for 72hr for knockdown by adding 600ng/ml doxycyclin.
|
| Growth protocol |
Kasumi-1 cells was cultured in RPMI 1640 supplemented with 10% FCS and 1% pen/strep at 37 °C and shRNA cell lines were culture in tet free FCS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was sonicated and used for ChIP seq using specific antibodies (avialable on suplementry table). RNA was extracted using qiagen rneasy and treated with ribozero kit.
ChIP seq libraries were preapared according to Illumina's standard protocol. For RNA-seq cDNA was prepared according to strand specific and libraries were preapared according to Illumina's standard protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
C3TCNACXX_2_5372
|
| Data processing |
Basecalls performed using CASAVA for both ChIP-seq and RNA-seq
Reads were aligned to the hg19 genome assembly (see characteristics) BWA for both ChIP-seq and RNA-seq
Peaks were called using MACS2 on settings: q 0.01
Genome_build: All ChIP-seq and RNA-seq tracks were mapped to genome build HG19
Supplementary_files_format_and_content: wig files were generated (extended to 300bps) with regions having more than 1 read in a window of 10 bps
|
| |
|
| Submission date |
Jan 01, 2016 |
| Last update date |
Nov 11, 2021 |
| Contact name |
Joost Martens |
| E-mail(s) |
j.martens@science.ru.nl
|
| Phone |
0243780645
|
| Organization name |
Radboud University
|
| Department |
RIMLS
|
| Lab |
Molecular Biology
|
| Street address |
Geert Grooteplein 28
|
| City |
Nijmegen |
| State/province |
Nederland |
| ZIP/Postal code |
6525GA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE76464 |
Epigenetic regulation of the apoptosis program in t(8;21) AMLs by an AML1-ETO, ERG and RUNX1 triad |
|
| Relations |
| BioSample |
SAMN04380939 |
| SRA |
SRX1514276 |
