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| Status |
Public on Jun 28, 2016 |
| Title |
GTPP sample 1 |
| Sample type |
SRA |
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| Source name |
HeLa cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
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| Extracted molecule |
total RNA |
| Extraction protocol |
NucleoSpin miRNA (Macherey-Nagel)
ribosomal depletion with RiboZero, directional RNA-seq library preparation, and 12 cycle amplification using LongAmp (New England BioLabs) and indexed primers (Integrated DNA Technologies)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Processing with the RNA-seq pipeline in http://bcbio-nextgen.readthedocs.org/en/latest/
FastQC
cutadapt
alignment with STAR
FastQC/RNA-SeQC
featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph files containing coverage data across the mitochondrial genome.
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| Submission date |
Nov 25, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christian Munch |
| E-mail(s) |
christian_munch@hms.harvard.edu
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| Organization name |
Harvard Medical School
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| Department |
Cell Biology
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| Street address |
240 Longwood Avenue
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| City |
Boston |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE75410 |
Mitochondrial unfolded protein response controls matrix pre-RNA processing and translation |
| GSE75411 |
Mitochondrial unfolded protein response controls matrix pre-RNA processing and translation |
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| Relations |
| BioSample |
SAMN04296146 |
| SRA |
SRX1452336 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1954527_T1.chrM.bedGraph.gz |
79.0 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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