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| Status |
Public on Oct 01, 2023 |
| Title |
Exosc3_mESC_cKO_TTseq_Rep1 |
| Sample type |
SRA |
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| Source name |
mESC
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| Organism |
Mus musculus |
| Characteristics |
genotype: Exosc3_cKO
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA extraction, cells were washed 3x with DPBS and lysed directly on the plate with 1mL of TRIzol reagent (Invitrogen, 15596026). Subsequently, RNA was purified using Direct-zol RNA Miniprep Plus Kits (Zymo, R2072) following manufacturer instructions. In brief, lysed cells in TRIzol were mixed 1:1 with 100% ethanol. Mixed lysates were added to the Zymo-spin columns, treated with DNase I, and washed with provided buffers. RNA was eluted with UltraPure DNase/RNase-Free Distilled Water (Invitrogen, 10977015).
250 ng of enriched RNA was used for library construction with the Illumina TruSeq stranded total RNA kit and Illumina CD index plate. After 5 cycles of PCR, samples were removed from the thermal cycler and a test PCR was performed to determine the optimal number of final cycles.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Adapters were trimmed from reads using Trim Galore (v0.5.0) (Martin, 2011). Reads were aligned to the GRCm38/mm10 reference genome using STAR (v2.7.5b) (Dobin et al., 2013) with the following custom parameters: --outFilterMultimapNmax 100 –winAnchorMultimapNmax 100. BAM files were filtered using sambamba (v.0.5.6), removing reads that are duplicated, unmapped, and removing all secondary alignments (i.e. keeping the best genomic alignment location for multimapping reads). BigWigs were generated on the filtered BAM files using deepTools (v3.5.0) (Ramirez et al., 2016) with RPKM normalization.
Assembly: mm10
Supplementary files format and content: TT-Seq coverage in bigWig format
Library strategy: TT-seq
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| Submission date |
May 31, 2022 |
| Last update date |
Oct 01, 2023 |
| Contact name |
Robert Sebra |
| E-mail(s) |
robert.sebra@mssm.edu
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| Organization name |
Icahn School of Medicine at Mount Sinai
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| Street address |
1 Gustave L. Levy Place
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE205197 |
RNA catabolism restricts ERV expression and functionalization [TT-seq] |
| GSE205211 |
RNA catabolism restricts ERV expression and functionalization |
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| Relations |
| BioSample |
SAMN28780790 |
| SRA |
SRX15510377 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6208434_Exosc3_mESC_cKO_TTseq_Rep1.bw |
404.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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