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| Status |
Public on Dec 25, 2013 |
| Title |
FibroblastVivo |
| Sample type |
SRA |
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| Source name |
Human fibroblasts
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Human fibroblasts
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| Treatment protocol |
300ul or 400 ul of DMS was added to 15mls of cells
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| Growth protocol |
cells were grown to 1million/ml(fibroblast) or OD=0.7 (yeast)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Triazol
RNA was randomply fragmented using Ambion fragmentation reagents. Fragments of 60-70mers were ligated to linker-1(IDTdna). Premature reverse transciptase producs were isolated by size selection. The cDNA was circularized with CircLigase(epicentre), and subjected to PCR for 8-10 cycles with primers for standard illumina sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
For human cells, stripped files were aligned to transcript model representing the longest splicing isoform, downloaded from RefSeq. For yeast cells, data was aligned to the yeast genome.
only uniquely aligned reads with less than two mismatches were taken.
Total counts per position per transcript were written to .txt files(human cells) or mapped to the yeast chromosomes in wig format
Genome_build: hg19(human cells) or yeast genome downloaded from yeastgenome.org on October11, 2009, corresponds to assembly R62 (UCSC: sacCer2)
Supplementary_files_format_and_content: txt files (human cells) and wig files (yeast cells). The processed data are .txt files and represents alignments to the transcriptome downloaded from RefSeq. For genes with multiple splicing isoforms, the longest isoform was used. Reads were filtered for 2 or less mismatches and unique alignments only. The txt file has three colums, 1= ref seq ID, 2=position , 3= number of aligned reads that passed filters
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| Submission date |
Dec 24, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Silvi Rouskin |
| E-mail(s) |
srouskin@wi.mit.edu
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| Organization name |
Whitehead Institute
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| Street address |
455 Main Street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02141 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE45803 |
Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo |
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| Relations |
| BioSample |
SAMN02485673 |
| SRA |
SRX398604 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1297506_Fibroblast_vivo.txt.gz |
29.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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