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| Status |
Public on May 25, 2021 |
| Title |
Dermal fibroblasts PID21_9124 |
| Sample type |
SRA |
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| Source name |
Dermal fibroblasts
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| Organism |
Homo sapiens |
| Characteristics |
cell line: ScienCell, 2310
treatment: miR-9/9*-124
cell type: Dermal fibroblasts
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| Growth protocol |
Direct neuronal reprogramming of human fibroblasts to neurons was performed as previously described (Abernathy et al., 2017; Richner et al., 2015).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Day 14 and day 21 cells were harvested for HITS-CLIP following the published protocol (Moore et al., 2014) with modifications. Briefly, cross-linked cells were lysed and treated with RQ1 DNase (Promega, M6101) and RNaseA (Thermo). Complex containing AGO-miRNA-mRNA were immunoprecipitated overnight at 4C with pan-AGO antibody. The immunoprecipitated complex was radio-labelled and extracted after running on NuPAGE gel (Thermo). RNA from the 130kDa band was extracted for sequencing using TruSeq Small RNA Library Preparation Kits (San Diego, CA).
TruSeq Small RNA Library Preparation Kits (San Diego, CA).
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Raw reads were aligned to human reference genome (GRCh38) by STAR (Dobin and Gingeras, 2015).
Counts were normalized by trimmed mean of M-values (TMM) using edgeR (Robinson et al., 2010).
Bigwig files were generated using bamCoverage (Ramírez et al., 2016).
Differential peaks using MACS (Feng et al., 2012; Zhang et al., 2008).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files of replicates for RNA-seq experiments
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| Submission date |
Nov 11, 2020 |
| Last update date |
May 25, 2021 |
| Contact name |
Ya-Lin Lu |
| E-mail(s) |
lu.y@wustl.edu
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| Organization name |
Washington University School of Medicine
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| Department |
Developmental Biology
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| Lab |
Andrew Yoo
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| Street address |
660 S. Euclide Avenue
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| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE161237 |
MiR-124 synergism with ELAVL3 enhances target gene expression to promote neuronal maturity [HITS-CLIP] |
| GSE161241 |
MiR-124 synergism with ELAVL3 enhances target gene expression to promote neuronal maturity |
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| Relations |
| BioSample |
SAMN16770453 |
| SRA |
SRX9474102 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4903828_PID21_9124.bw |
22.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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