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| Status |
Public on Nov 08, 2019 |
| Title |
HPC-7_Control_Rep3 |
| Sample type |
SRA |
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| Source name |
HPC-7
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| Organism |
Mus musculus |
| Characteristics |
cell line: HPC-7
condition: Control
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| Treatment protocol |
Hsp90 inhibition was carried out using the following concentrations of NVP-AUY922 for 16h hours with the corresponding cell types: 50nM for HPC-7, 200nM for MEFs and 300nM for K562.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was done using TRI-Reagent (Sigma Aldrich, #T9424) according to manufacturer’s.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
RawCounts_HPC7_HSP90i.txt
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| Data processing |
RNA-seq reads were trimmed with TrimGalore (http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/, v0.4.0) and mapped to Gencode (GRCh37, release: 19 or GRCm38, release m4, respectively) annotation using TopHat2 (Kim, Pertea et al. 2013) (v2.0.13) with the options mate- inner-dist, mate-std-dev and library-type (fr- firststrand). The distance between read mates (mate-inner- dist [http://broadinstitute.github.io/picard.] (v1.1.21). After mapping of the RNA-seq reads from all samples, the reads that mapped uniquely to the genome were counted using featureCounts (Liao, Smyth et al. 2014) with the following options: -Q 10 -p -B -C -s 2. The annotations present in the Homo sapiens gtf file from the Ensembl release 75 were used as reference for counting. DESeq2 (Love, Huber et al. 2014) was used for differential expression analysis of all replicates for each condition. Genes with an adjusted P value < 0.01 and absolute log2 fold change more than 1 were defined as significantly affected.
ChIP-seq reads were aligned to the human genome build hg38 or mouse genome mm10, respectively, using Bowtie2 (Langmead and Salzberg 2012). Duplicate and discordant reads were removed. Peak calling was done with MACS2 (model- based analysis of ChIP- Seq) (Zhang, Liu et al. 2008) using "-- keep-dup all", "--nomodel" and "--extsize 200". Gene annotations and transcript start site (TSS) information for human genes were from taken from Gencode annotation release 26 and for mouse genome from Gencode annotation release m4. For visualization, the paired-end reads were extended to fragment size and normalized to total reads aligned (reads per million, rpm) using deeptools2 (Ramirez, Ryan et al. 2016). Profile plots and heatmaps of ChIP-seq signal were generated with deeptools2 (Ramirez, Ryan et al. 2016).
Genome_build: hg38 / mm10
Supplementary_files_format_and_content: Text file with raw RNA-seq read counts in Control and upon HSP90 inhibition per cell type.
Supplementary_files_format_and_content: Text file with HSP90 ChIP-seq peaks in K562 cells.
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| Submission date |
Feb 06, 2019 |
| Last update date |
Nov 08, 2019 |
| Contact name |
Barbara Hummel |
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
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| Street address |
Stübeweg 51
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| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE126151 |
A systematic analysis of nuclear heat-shock protein 90 identifies a metazoan-specific regulatory module |
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| Relations |
| BioSample |
SAMN10880622 |
| SRA |
SRX5342017 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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