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| Status |
Public on Oct 31, 2012 |
| Title |
RNA 03-03, F |
| Sample type |
SRA |
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| Source name |
fibroblast
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| Organism |
Homo sapiens |
| Characteristics |
passage number: 2
cell type: fibroblast
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| Growth protocol |
Fibroblast were growth under standar condition in DMEM high Glucose media containing 10% FBS. iPSCs were mantained on matrigel coated plates in DMEM/F12 media containing 1% N2 supplement, 2% B27 supplement, 2 mM L-glutamine, 0.1 mM non-essential amino acids, 1% penicillin/ streptomycin, 0.5 mg/mL BSA Fraction V, 0.12 mM monothioglycerol. Colonies were passed using dispase.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were treated with Accutase and pelleted. Total RNA was extracted using PicoPure kit (Life Technologies catalog # KIT0204).
Fibroblast RNA libraries for both families (03 and 1123) were prepared for sequencing using standard Illumina protocols using 5 ug of total RNA. iPSC RNA libraries for family 03 were prepare as well using standard Illumina protocols using 2.5 ug of total RNA. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2.5 ug of total RNA for the construction of multiplex sequencing libraries for all iPSC for members of family S1123. In all cases, library fragments of ~300 bp were band isolated from an agarose gel.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
ILLUMINA HiSeq sequencing reads
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| Data processing |
Base calling: Illumina CASAVA
Alignment: Tophat 1.3.1, parameters --solexa1.3-quals --coverage-search --no-novel-indels --microexon-search [extra parameter "-r 100" for PE 2x100 data, "-r 150" for 2x75 data and without "-r" parameter for SE data]
Conversion from BAM to SAM: SAMtools 0.1.11
Conversion SAM to MRF: sam2mrf (part of RSEQtools, couldn't find RSEQtools version, it is whatever version was available as of August 2011)
RPKM computation: mrfQuantifier (part of RSEQtools, same note about version)
Genome_build: hGRC37 (hg19)
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| Submission date |
Oct 19, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Flora Vaccarino |
| Organization name |
Yale University
|
| Department |
Child Study Center
|
| Lab |
Vaccarino
|
| Street address |
230 South Frontage Road
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06520 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE41716 |
Somatic copy-number mosaicism in human skin revealed by induced pluripotent stem cells (sequencing) |
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| Relations |
| SRA |
SRX198060 |
| BioSample |
SAMN01773274 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1023067_F03-03_110325_MAGNUM_00063_FC631P1_L3.rpkm.gz |
251.6 Kb |
(ftp)(http) |
RPKM |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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