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Sample GSM759868 Query DataSets for GSM759868
Status Public on Mar 16, 2012
Title E10.5_forelimb_mRNA_seq_rep1
Sample type SRA
Source name embryonic forelimb bud, RNA-Seq
Organism Mus musculus
Characteristics strain: C57BL/6J
tissue: forelimb bud
developmental stage: gestational day E10.5
sequencing run type: Single-end 35
Treatment protocol Pregnant mothers were euthanized, and embryos were removed and placed in cold PBS. Forelimb and hindlimb buds were individually removed with forceps.
Growth protocol Normal mouse gestation to day 10.5.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with the RNeasy kit (Qiagen).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
Description polyA-selected RNA
Data processing RNA-Seq alignments and counts: RNA-Seq reads were aligned with bowtie (0.12.3) to the mouse genome (mm9) retaining only uniquely mapped reads ( command: bowtie -m 1 -B 1 --solexa1.3-quals --sam --sam-nohead ~/GENOME/mm9/dna/mm9_nh+splice30). Bowtie output was converted to tophatSAM format for use with Cufflinks for calculation of gene expression (RPKM).
Submission date Jul 13, 2011
Last update date May 15, 2019
Contact name Justin Cotney
Organization name UConn Health
Department Genetics and Genome Sciences
Lab Cotney Lab
Street address 400 Farmington Ave.
City Farmington
State/province CT
ZIP/Postal code 06030-6403
Country USA
Platform ID GPL11002
Series (1)
GSE30641 Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb.
SRA SRX083279
BioSample SAMN00668318
Named Annotation

Supplementary file Size Download File type/resource 220.7 Mb (ftp)(http) BW
GSM759868_E10.5_forelimb_mRNA_seq_rep1.tophat.SAM.gz 330.6 Mb (ftp)(http) SAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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