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| Status |
Public on Feb 25, 2017 |
| Title |
Ribo-Zero total RNA CCE 2 |
| Sample type |
SRA |
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| Source name |
Day5 differentiated CCE
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| Organism |
Mus musculus |
| Characteristics |
strain: 129/SvEv
cell type: differentiated ES cells induced by retinoic acid for 5 days
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| Treatment protocol |
Cell were treated as described: Huang et al., PLoS ONE 2011, PMID: 22102886
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| Growth protocol |
Cell were cultured and tissues obtained as described: Huang et al., PLoS ONE 2011, PMID: 22102886
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared as described: Huang et al., PLoS ONE 2011, PMID: 22102886
Libraries were prepared as described: Huang et al., PLoS ONE 2011, PMID: 22102886
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Ribo-Zero total RNA, Trizol isolated
processed data file: CCE.RefSeq_read_count.txt
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| Data processing |
Reads from each fastq file for CCE (reads provided here and from GSM718982) and fetal head (reads provided here and from GSM718983) were trimmed using trimmomatic v0.32 with these parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
All reads passing the filtering criteria were aligned using STAR v2.3 as single reads (paired information was not used), separtely for each tissue using these parameters: --outStd SAM, --outSAMmode Full, --alignIntronMax 200000, --outFilterIntronMotifs RemoveNoncanonical, --outSAMstrandField intronMotif, --outFilterMultimapNmax 1.
SAM output was converted to bam and sorted by position using samtools v 0.1.19. Reads Per Kb per Millions of reads (RPKM) expression values were calculated using the RPKM_count.py script from RSeQC v2.3.9 using the -u –e parameters.
Annotation: NCBI RNA reference sequences collection (RefSeq) obtained from the UCSC genome browser on the 17.07.2014
Genome_build: mm10
Supplementary_files_format_and_content: text file with tab delimitted output from RPKM_count.py
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| Submission date |
Nov 27, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Florian M Pauler |
| E-mail(s) |
florian.pauler@ist.ac.at
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| Phone |
+43 2243 9000-7434
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| Organization name |
IST Austria
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| Lab |
Simon Hippenmeyer
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| Street address |
Am Campus 1
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| City |
Klosterneuburg |
| ZIP/Postal code |
3400 |
| Country |
Austria |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE75453 |
RNA-Seq to compare gene expression to MIRTA tiling arrays |
| GSE75454 |
Transcript identification and quantification on Mouse Imprinted Region Tiling Array (MIRTA) |
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| Relations |
| BioSample |
SAMN04298993 |
| SRA |
SRX1453423 |
| 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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