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Sample GSM1286170 Query DataSets for GSM1286170
Status Public on Mar 22, 2018
Title d4 M2 sRNA-2
Sample type SRA
 
Source name differentiating ES cells
Organism Mus musculus
Characteristics cell type: differentiating ES cells
strain: 129 x castaneus
developmental stage: day 4
Extracted molecule total RNA
Extraction protocol The NEBNext Small RNA Sample Prep Set 1 (Illumina Compatible) library construction protocol was followed (NEB #E6120S/L), along with the SMART kit and Nextera kit for Illumina sequencing for RNA-seq libraries.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
 
Data processing Sequencing adapters were removed from reads by finding the 3'-most complete match to the adapter sequence and trimming the read after that position.
Reads were first mapped to the collection of ribosomal repeats (annotated using the repeatMasker file downloaded from the UCSC genome browser), snoRNAs and snRNAs in the mouse genome (version mm9) using Bowtie (version 0.12.7) in order to remove common contaminants.
The unmapped reads from this filtering step were then mapped against the mm9 genome.
Genome_build: mm9
 
Submission date Dec 10, 2013
Last update date May 15, 2019
Contact name Diane E Trout
Organization name California Institute of Technology
Department Biology
Lab Wold
Street address 1200 E California Blvd M/C 156-29
City Pasadena
State/province CA
ZIP/Postal code 91125
Country USA
 
Platform ID GPL13112
Series (1)
GSE39884 Small RNAs in undifferentiated and differentiating mouse embryonic stem cells
Relations
BioSample SAMN02469164
SRA SRX396270

Supplementary data files not provided
SRA Run SelectorHelp
Processed data not provided for this record
Raw data are available in SRA

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