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Status |
Public on Feb 25, 2017 |
Title |
Ribo-Zero total RNA fetal head 1 |
Sample type |
SRA |
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Source name |
14.5dpc fetal head
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Organism |
Mus musculus |
Characteristics |
strain: FVB/N cell type: fetal head dissected from 14.5dpc mouse embryo
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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 |
GSM718983 Ribo-Zero total RNA, Trizol isolated processed data file: FH.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 |
Reanalysis of |
GSM718983 |
BioSample |
SAMN04298994 |
SRA |
SRX1453424 |
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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