|
| Status |
Public on Mar 09, 2021 |
| Title |
ChIP-seq: GSC11 NS H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
glioblastoma stem cell
|
| Organism |
Homo sapiens |
| Characteristics |
glioblastoma stem cell culture: GSC11
cell type: Glioblastoma stem cells
chip antibody: H3K4me3 (Diagenode 03-050)
treatment: non targeting shRNA
|
| Treatment protocol |
SMART vector non targeting PGK-TurboGFP (VSC11713) was purchased from GE Healthcare (Little Chalfont, UK). Viral particles were produced and concentrated by the Vectorology platform of Montpellier (Biocampus, Montpellier, France). GSCs were infected using a multiplicity of infection of 10 and processed 120 h later for ChIP-seq analysis
|
| Growth protocol |
Glioblastoma stem cells were cultured in Neurobasal Medium supplemented with B27 1%; N2 0.5%; bFGF 0.05% and EGF 0.005% at 37°C in 5% CO2 humidified incubator. Culture medium was replaced twice a week and when spheres became large and numerous, they were enzymatically dissociated with accutase. Glioblastoma stem cell cultures were characterized by assessing self renewal, differentiation and tumorigenic ability as well as their expression of stemness markers (CD133, SOX2). Finally, all cultures were also classified according to Verhaak's classification of glioblastomas using the method of classification to nearest centroids (ClaNC) with a 840 gene signature.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq were performed on native chromatin isolated from frozen GSC pellets
Library preparation and sequencing on NovaSeq 6000 (Illumina) were performed by IntegraGen SA, according to the manufacturer’s recommendations
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
ChIP-seq R1 reads were mapped to the human genome (hg19) using Bowtie2 (v 2.3.4.3).
Alignments were filtered according to their quality (Mapq>30) using SamTools (v 1.9) .
ChIP-seq signals coverage were generated with Bamcoverage (v 3.1.3) (options: normalizeUsing RPKM, extendReads 200, ignoreDuplicates, binSize 20)
Peak detection was carried out with MACS (v 1.4.2) using Input as a control (options: nomodel shiftsize 73, for H3K27ac and H3K4me3 pvalue= 1e-5 , for H3K27me3 pvalue= 1e-3).
Genome_build: hg19
Supplementary_files_format_and_content: coverage signal; bigwig
|
| |
|
| Submission date |
Nov 13, 2020 |
| Last update date |
Mar 09, 2021 |
| Contact name |
franck court |
| Organization name |
GReD CNRS
|
| Street address |
28 Place Henri Dunant
|
| City |
Clermont-Ferrand |
| ZIP/Postal code |
63000 |
| Country |
France |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE161436 |
Chromatin states in glioblastoma stem cell [ChIP-seq] |
| GSE161440 |
Chromatin states and Transcriptome in in glioblastoma stem cells |
|
| Relations |
| BioSample |
SAMN16793089 |
| SRA |
SRX9505485 |
