|
Status |
Public on Jan 07, 2016 |
Title |
129SvEv primed |
Sample type |
SRA |
|
|
Source name |
primed EpiSC
|
Organism |
Mus musculus |
Characteristics |
strain: 129SvEv 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 129SvEv 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 |
|
Relations |
BioSample |
SAMN03280112 |
SRA |
SRX835025 |