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| Status |
Public on Apr 01, 2015 |
| Title |
RNAomeSeq_8.4.16 |
| Sample type |
SRA |
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| Source name |
Embryonic Stem cell
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| Organism |
Mus musculus |
| Characteristics |
cell type: HPRT deficient ES cells
treatment: Control
passage: 19-22
strain: C57BL/6
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| Treatment protocol |
2.5uM of Cisplatin or DMSO (volume equal of 100%) was added to the medium
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| Growth protocol |
Cells were grown for 2 passages on feeder coated plates and 1 pasage on gelatin coated plates before taken into experiment
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| Extracted molecule |
total RNA |
| Extraction protocol |
miRNeasy kit (qiagen) used to extract Total RNA
RNAomeSeq library preparation was performed using our own protocol. Total RNA was depleted of ribosomal RNA (RiboMinus, Life science) and subsequently fragmented (Covaris S200). Adapters were ligated to the fragmented rRNA depleted RNA pool (adapters from the TruSeq smallRNA kit v1.5) and cDNA was made by reverse transcriptase. After amplification of the cDNA (11 cycli) the RNA was fractionated to sizes of 15-500nt by gel.
Indexes used for mRNASeq and RNAomeSeq (CGATGT: 8.3.3, TGACCA: 8.4.3, ACAGTG: 8.5.3, GCCAAT: 8.4.16, CAGATC: 8.5.16, CTTGTA: 8.6.16) and smallRNASeq (CGATGT: 8.3.3, TGACCA: 8.4.3, ACAGTG: 8.5.3, CGATGT: 8.4.16, TGACCA: 8.5.16, ACAGTG: 8.6.16)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
RNAome sequencing is a method to sequence small and large RNA species from ribosomal RNA-depleted total RNA in a single run.
rRNA depleted total RNA
RNAomeSeq_longRNA_expression.txt
RNAomeSeq_longRNA_abundance.txt
RNAomeSeq_smallRNA_expression_abundance.txt
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| Data processing |
Base-calling and alignment was performed with NARWAL [ref]
Bowtie, TopHat,Cufflings, sequence adapter trimming
Reads, from Bam files containing reads 36 nucleotide of length aligned, were extracted from mm9 RefSeq annotated exonic and non-exonic region, exonic reads were summed per transcript
Reads, smaller then 36 nucleotide of length due to adapter trimming from readcount files, were aligend to miRbase v19, tRNA and 5/5.8s rRNA sequences using the R bioconductor package Biostrings.
Abundancy was calculated by extracting primary aligned reads (ScanBamParam(IsNotPrimaryRead=FALSE)) or unique small reads
Regions or reads were called expressed when present above a threshold in all biological replicates in at least one of the two experimental groups.
Statistical analysis of expressed regions or reads was performed with the R bioconductor package EdgeR
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited files containing expression of regions/transcripts or abundance (unique presence or alignment) of regions/transcripts.
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| Submission date |
Jun 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kasper Derks |
| E-mail(s) |
[email protected]
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| Organization name |
Maastricht University Medical Center
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| Department |
Clinical Genetics
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| Street address |
P. Debyelaan 25
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| City |
Maastricht |
| State/province |
Limburg |
| ZIP/Postal code |
6229 HX |
| Country |
Netherlands |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE48083 |
Deciphering the RNA landscape by RNAome sequencing [Seq] |
| GSE48084 |
Deciphering the RNA landscape by RNAome sequencing |
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| Relations |
| BioSample |
SAMN02207786 |
| SRA |
SRX310168 |
| 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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