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| Status |
Public on Jan 07, 2016 |
| Title |
rat naïve |
| Sample type |
SRA |
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| Source name |
naïve iPS
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| Organism |
Rattus norvegicus |
| Characteristics |
cell state: naïve
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
naïve iPS cells from rat
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| 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
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| Submission date |
Jan 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jenny Chen |
| Organization name |
Harvard
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| Street address |
16 Divinity Ave
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| City |
Cambridge |
| ZIP/Postal code |
02138 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE64818 |
Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs |
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| Relations |
| BioSample |
SAMN03280113 |
| SRA |
SRX835030 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1581179_rat.naive.coding.fpkm.txt.gz |
616.3 Kb |
(ftp)(http) |
TXT |
| GSM1581179_rat.naive.lnc.fpkm.txt.gz |
16.3 Kb |
(ftp)(http) |
TXT |
| GSM1581179_rat.naive.wig.gz |
86.9 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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