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| Status |
Public on Aug 28, 2013 |
| Title |
Unfused fibroblast rep1 |
| Sample type |
SRA |
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| Source name |
Unfused Human Fib
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| Organism |
Homo sapiens |
| Characteristics |
sample type: Unfused Human Fib
cell line(s): human fibroblast
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
At least 30,000 heterokaryons were FACS sorted and total RNA was extracted using the Qiagen RNeasy Micro Kit. Poly A enrichment was performed with Oligo dT bead selection. The resulting poly-A+ RNA was fragmented and cDNA was synthesized using Superscript II and random primers.
Libraries were prepared according to standard Illumina protocol, using the NEB Next modules for library construction.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Homo sapiens
Fib1 BC12
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence to 50bp and mapped to hg19 and mm10 after removal of mouse and human rRNA sequences.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using SeqMap. Reads mapping to both organisms were removed. To account for removal of the homologous reads, a mathematical correction was introduced to calculate the effective transcript length (exon length) in which the "effective transcript length" is equal to the "original transcript length - 50bp - 1bp for every unique 50bp sequence read which matched perfectly between mouse and human" for that particular transcript.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: .txt files include mouse and human RPKM values for each Sample. Transcripts with RPKM values of zero have been removed.
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| Submission date |
Jan 16, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jennifer Brady |
| Organization name |
Stanford University
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| Street address |
269 Campus Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
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| Relations |
| SRA |
SRX217762 |
| BioSample |
SAMN01888207 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1065162_Fib1_BC12.txt.gz |
99.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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