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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 02, 2019 |
| Title |
RNAseq-parental_NT_rep2 |
| Sample type |
SRA |
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| Source name |
3617 parental cells, non-treated, RNA
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| Organism |
Mus musculus |
| Characteristics |
cell line: Parental
cell type: mouse adenocarcinoma
treatment: no treatment
concentration: NA
time: NA
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| Treatment protocol |
Mouse adenocarcinoma and MEF cells were grow in steroid-depleted medium (10% charcoal stripped FBS in DMEM) for 24 h, and the cells were subsequently left untreated or treated 100 nM of dexamethasone for 1 h in ChIP-seq and ATAC-seq, and for 2 h in RNA-seq, prior extraction.
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| Growth protocol |
Mouse adenocarcinoma and MEF cells were grown in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 25 U/ml penicillin and 25 µg/ml streptomycin, and 2mM L-Glutamine, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator. Mouse adenocarcinoma cells were also supplemented with 5 µg/ml of tetracycline to supress GFP-GR expression.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For ChIP-seq, lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with specified antibody. For ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Nextera Tn5 Transposase from Nextera kit. For RNA-seq, RNA was extracted using the PureLink RNA mini kit.
Libraries were prepared for sequencing using standard Illumina protocols.
For ChIP-seq, Illumina TruSeq Chip Sample Prep Kit; for ATAC-seq, Illumina Nextera DNA Library Prep Kit; for RNA-seq, Illumina Stranded Total RNA.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
RTA 2.4.11 was used for Basecalling and Bcl2fastq 2.17 was used for demultiplexing allowing 1 mismatch.
Trimmomatic 0.36 was used for adapter and quality control
ChIP- and ATAC-seq alignment was performed by Bowtie2 (2.1.0) with Bowtie2 –p 8 –x bowtie2_ref/genome_prefix –U read1.fastq –S result.sam.
RNA-seq alignment was performed by TopHat (2.0.8) with tophat -G annotation.gtf -o ./ -r 10 --mate-std-dev 200 -p 16 --librarytype fr-firststrand bowtie2_annotation/prefix read1.fastq read2.fastq
Peaks were called using HOMER program version 4.9 with findPeaks with following parameters; FDR<0.001, 4x fold enrichment over control, 4x fold enrichment over local background, and >75 tags per site. In addition, untreated GR ChIP sample was used to further filter out noise from GR samples using default parameters on getDifferentialPeaks.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph (HOMER makeUCSCfile command) from alignment file.
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| Submission date |
Feb 27, 2018 |
| Last update date |
Apr 03, 2019 |
| Contact name |
Ville Paakinaho |
| E-mail(s) |
villepaakinaho@gmail.com
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| Organization name |
University of Eastern Finland
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| Department |
School of Medicine
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| Lab |
Biomedicine
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| Street address |
Yliopistonranta 8
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| City |
Kuopio |
| ZIP/Postal code |
70210 |
| Country |
Finland |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE108634 |
Glucocorticoid Receptor Quaternary Structure Drives Chromatin Occupancy and Transcriptional Outcome |
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| Relations |
| BioSample |
SAMN08618442 |
| SRA |
SRX3747941 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3025252_RNAseq-parental_NT_rep2.ucsc.bedGraph.gz |
293.1 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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