GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1955409 Query DataSets for GSM1955409
Status Public on Feb 25, 2017
Title Ribo-Zero total RNA fetal head 2
Sample type SRA
Source name 14.5dpc fetal head
Organism Mus musculus
Characteristics strain: FVB/N
cell type: fetal head dissected from 14.5dpc mouse embryo
Treatment protocol Cell were treated as described: Huang et al., PLoS ONE 2011, PMID: 22102886
Growth protocol Cell were cultured and tissues obtained as described: Huang et al., PLoS ONE 2011, PMID: 22102886
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
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description Ribo-Zero total RNA, Trizol isolated
processed data file: FH.RefSeq_read_count.txt
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 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
Submission date Nov 27, 2015
Last update date May 15, 2019
Contact name Florian M Pauler
Phone +43 2243 9000-7434
Organization name IST Austria
Lab Simon Hippenmeyer
Street address Am Campus 1
City Klosterneuburg
ZIP/Postal code 3400
Country Austria
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)
BioSample SAMN04298995
SRA SRX1453425

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap