|
| Status |
Public on May 01, 2024 |
| Title |
Sample 21_DIPGXIII, ChIP-seq H3.3, DMSO |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: brain
cell line: DIPGXIII
antibody: H3.3
genotype: H3.3K27M mutant
treatment: DMSO
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA-seq: RNA was isolated using RNeasy Plus Kit (Qiagen) according to manufacturer’s instructions and the quality was assessed with the Agilent 2100 Bioanalyzer with an RNA 6000 Pico Kit (Agilent Technologies).
RNA-seq: PolyA-enriched RNA libraries were prepared with the KAPA Stranded mRNA Sample Preparation Kit (Kapa Biosystems).
ChIP-seq: ChIP-seq (including crosslinikng, cell lysis, chromatin digestion with Mnase, and chromatin immunoprecipitatation with H3.3 and H3.3K27M antibodies) was performed based on protocol by Cook et al.., 2017 (doi: 10.1002/cpmb.45). Eluted and input DNA was purified with phenol-chloroform extraction followed by additional purification with ZymoResearch DNA Clean & Concentrator-5 columns. Digested DNA profiles were confirmed using the 2100 Bioanalyzer with the Agilent DNA High Sensitivity chip (Agilent Technologies).
ChIP-seq: The Input and ChIP libraries were prepared using the Qiaseq Ultra Low Input Library Kit (Qiagen), according to manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RNAseq: The sequenced paired-end reads were mapped to hg38 genome using tophat2 aligner v2.1.1 with the default parameters. The expression estimates for each gene were obtained using Bioconductor package DESeq2. TPM (Transcripts per Kilobase Million) values were calculated
ChIPseq: The paired-end fragments were generated. Reads were mapped to the to hg38 genome using Bowtie aligner version 0.12.9. Only uniquely mapped reads were retained. The reads with insert sizes <50 bp or >500 bp were removed from further analysis. Genomic positions with the numbers of mapped tags above the significance threshold of Z-score of 7 were identified as anomalous, and the tags mapped to such positions were discarded. H2A.Z, H3.3 and H3.3K27M occupancies were estimated as tag frequencies
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each RNA-seq sample
Supplementary files format and content: ChIPseq: wig files with coverage
|
| |
|
| Submission date |
May 11, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Jakub Mieczkowski |
| E-mail(s) |
jmieczkowski@jmieczkowski.pl
|
| Organization name |
Medical University of Gdansk
|
| Street address |
Debinki 12
|
| City |
Gdansk |
| ZIP/Postal code |
80-211 |
| Country |
Poland |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE232283 |
H2A.Z histone variants facilitate HDACi-dependent removal of H3.3K27M mutant protein in paediatric high-grade glioma cells |
|
| Relations |
| BioSample |
SAMN35041384 |
| SRA |
SRX20292514 |
