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Sample GSM1581176 Query DataSets for GSM1581176
Status Public on Jan 07, 2016
Title NOD primed
Sample type SRA
Source name primed EpiSC
Organism Mus musculus
Characteristics strain: NOD
cell state: epiblast
Extracted molecule total RNA
Extraction protocol Briefly, 10ug of total RNA was polyA selected twice using Oligo(dT)25 beads (Life Technologies) and NEB oligo(dT) binding buffer.
PolyA-selected RNA was fragmented, repaired and cleaned using Zymo RNA concentrator-5 kit. 30ng of polyA-selected RNA per sample were used to make RNA-seq libraries. Adapter was ligated to RNA, RNA was reverse transcribed and second adapter was ligated on cDNA.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description primed epiSCs from NOD mouse
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and aligned using TopHat v2.0.10 (-N 3 --read-edit-dist 3 --library-type fr-secondstrand --prefilter-multihits --max-multihits 15 --segment-length 20). Optical duplicates were removed using Picard's MarkDuplicates utility
Transcripts were reconstructed from TopHat alignments using Scripturev3.1 (-coverage 0.2)
Fragments per Kilobase of exon per Megabase of library size (FPKM) was calculated using Cufflinks v2.1.1
Genome_build: mm9, rn5, hg19
Supplementary_files_format_and_content: tab-delimited text file of cufflinks estimation of coding gene FPKMs
Supplementary_files_format_and_content: tab-delimited text file of cufflinks estimation of lncRNA FPKMs
Supplementary_files_format_and_content: wig file representing RNA-Seq coverage of aligned reads
Submission date Jan 09, 2015
Last update date May 15, 2019
Contact name Jenny Chen
Organization name MIT
Department Health Sciences and Technology
Street address 77 Mass Ave
City Cambridge
ZIP/Postal code 02142
Country USA
Platform ID GPL17021
Series (1)
GSE64818 Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs
BioSample SAMN03280115
SRA SRX835027

Supplementary file Size Download File type/resource
GSM1581176_mouse.nod.primed.coding.fpkm.txt.gz 599.6 Kb (ftp)(http) TXT
GSM1581176_mouse.nod.primed.lnc.fpkm.txt.gz 12.9 Kb (ftp)(http) TXT
GSM1581176_mouse.nod.primed.wig.gz 73.0 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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