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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 28, 2016 |
| Title |
ES_shTet1-2 [small RNA-seq] |
| Sample type |
SRA |
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| Source name |
ES_shTet1_small RNA-seq
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| Organism |
Mus musculus |
| Characteristics |
cell line: E14
strain background: 129/Ola
cell type: embryonic stem (ES) cells
shRNA: shTet1
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| Treatment protocol |
Lentiviral particles containing pLKO.1 shRNA vectors were produced by standard methods in 293T cells. Transduced ES cells were selected with 1 µg/ml puromycin 24 hours post-infection and collected after 3 days of selection.
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| Growth protocol |
ESCs were cultured on gelatin-coated plates without feeders, in DMEM-based media (Gibco 10569010) supplemented with 15% fetal bovine serum, pen/strep, nonessential amino-acids, beta-mercaptoethanol and 1,000 U/ml LIF (Millipore).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using either QIAzol (QIAGEN) or the Quick-RNA Midiprep kit (Zymo).
Libraries were prepared using the NEBNext small RNA library prep kit (NEB), followed by size selection (~120-150 bp, including adaptors) using gel extraction.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Adaptors were trimmed using trim_galore! v0.3.3 with the options ‘-q 0 --length 15’.
Trimmed reads were mapped to mm9 using bowtie2 v2.1.0 with default parameters, which reports multi-hit read alignments.
Reads in the size range of 19-32 nt that overlapped full-length (>5 kb) LINE1 elements were extracted and annotated with the respective LINE1.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with the following fields: SAM file ‘flag’ denoting a top (0) or bottom (16) strand alignment, read sequence (‘read’), read coordinates (‘chr.read’, ‘start.read’, ‘end.read’), LINE1 coordinates (‘chr’, ‘start’, ‘end’), LINE1 ‘class’, LINE1 orientation (‘strand’).
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| Submission date |
Jul 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Miguel R Branco |
| E-mail(s) |
m.branco@qmul.ac.uk
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| Organization name |
Blizard Institute
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| Street address |
4 Newark Street
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| City |
London |
| ZIP/Postal code |
E1 2AT |
| Country |
United Kingdom |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE84459 |
TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells [small RNA-seq] |
| GSE84460 |
TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells |
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| Relations |
| BioSample |
SAMN05406770 |
| SRA |
SRX1951456 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2236641_shTet1-2_LINE1_reads.txt.gz |
243.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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