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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 07, 2018 |
| Title |
Sample_KP-RNA-66Q-3 |
| Sample type |
SRA |
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| Source name |
293T cells
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| Organism |
Homo sapiens |
| Characteristics |
lentiviral mediated overexpression: mHTT
cell line: 293T cells
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| Treatment protocol |
Cells were harvested 3 days after LV transduction.
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| Growth protocol |
All cell culture work on 293T cells was performed as described before (Musiwaro, P., Smith, M., Manifava, M., Walker, S.A. & Ktistakis, N.T. Characteristics and requirements of basal autophagy in HEK 293 cells. Autophagy 9, 1407-1417 (2013)). Cells were grown to ≈ 80 % confluence in six well plates before harvesting.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the miRNeasy Mini kit from Qiagen
KAPA Stranded mRNA-Seq Kit from KAPAbiosystems
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
non treated (NT), samples colleceted 3 days after LV transduction
featC.polyAinvitrorefseq.txt
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| Data processing |
Adaptor sequences were removed using cutadapt
Reads from samples obtained from 293T cells were aligned to the human genome, reads obtained from mouse tissue were mapped to the mouse genome using STAR_2.4.0j (default settings for mRNA, for microRNAs 2 mismatches per 20nt were allowed)
Reads were quantified using the Rsubread package for R using miRbase annotation (miRNAs), refseq annotations (for mRNA) and Ensembl (for snoRNA and snRNA)
Genome_build: hg19 for 293T cells; mm10 for mouse tissue
Supplementary_files_format_and_content: txt files containing abundance measurements of miRNA features from miRBase / snoRNA, snRNA features from Ensembl/ refseq features for mRNA. Whitespace separated. Columns: [Geneid- Chr- Start- End- Strand- Length - #reads mapping to feature]
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| Submission date |
Mar 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Per Brattas |
| Organization name |
Lund University
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| Lab |
Clinical Genomics
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| Street address |
Sölvegatan 17
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| City |
Lund |
| ZIP/Postal code |
221 84 |
| Country |
Sweden |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE78928 |
Huntingtin aggregation impairs autophagy leading to Argonaute-2 accumulation and global microRNA dysregulation |
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| Relations |
| BioSample |
SAMN04535108 |
| SRA |
SRX1615459 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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