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| Status |
Public on Oct 23, 2013 |
| Title |
Human smRNA iPSC1 |
| Sample type |
SRA |
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| Source name |
induced pluripotent stem cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: iPSC
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| Growth protocol |
Human iPSC lines WT-33 and ADRC-40 (human IPSC1 and IPSC2 in this work, respectively) and WT-126 were previously described (Marchetto et al., 2010). Fibroblasts from human GM22159 (WT-9), Pan troglodytes (Chimpanzees: PR00818 and PR01209) and from Pan paniscus (Bonobos: AG05253 and PR01086) were acquired from Coriell Cell Repositories (NJ). All fibroblasts were cultured in Minimum Essential Medium (Invitrogen) supplemented with 10% fetal bovine serum (HyClone Laboratories). Retroviral vectors expressing Oct4, c-Myc, Klf4 and Sox2 human cDNAs from Yamanaka's group were obtained from Addgene. Recombinant viruses were produced by transient transfection in 293T cells. Two days after infection, cells were plated on mitotically inactivated mouse embryonic fibroblasts (Chemicon) with hESC medium. After 3 weeks, iPSCs colonies were picked manually and directly transferred to feeder-free conditions on matrigel-coated dishes (BD) using mTeSRTM1 (StemCell Technologies). Established iPSCs colonies were tested for karyotype integrity and expression profile of undifferentiatied markers. Cells were kept in feeder-free conditions indefinitely and passed using mechanical dissociation.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was extracted from ~5x106 cells using the RNeasy Plus kit (Qiagen, Valencia, CA), according to the manufacturer's instructions.
Small RNA (15-40 nt) libraries were prepared using the Illumina TruSeq Small RNA sample preparation kit and sequenced on an Illumina HiSeq 2000 sequencer (Single end 50 bp)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
small RNA
small RNA-Seq (strand specific)
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| Data processing |
Adapter sequences were trimmed from all single-end reads and mapped to the human (hg19, GRCh37) genome using bowtie2 (v2.1.0). To calculate miRNA expression, reads with 5' ends mapping to miRBase transcripts where found using HOMER
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file with normalized read count totals for miRNAs found in miRBase (hg19 assembly)
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| Submission date |
Sep 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher Benner |
| E-mail(s) |
cbenner@ucsd.edu
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| Organization name |
University of California, San Diego (UCSD)
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| Department |
Medicine
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| Street address |
9500 Gilman Dr. MC 0640
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| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093-0640 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE47626 |
Differential LINE-1 retrotransposition in induced pluripotent stem cells between humans and great apes |
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| Relations |
| BioSample |
SAMN02353799 |
| SRA |
SRX348430 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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