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| Status |
Public on Jun 20, 2019 |
| Title |
endo_KO_13 [E8] |
| Sample type |
SRA |
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| Source name |
Uterus
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| Organism |
Mus musculus |
| Characteristics |
genotype: Plag1KO
tissue: endometrium
mouse id: 13
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| Treatment protocol |
Sexually mature Plag1KO and WT females were superovulated by i.p. injections of 5 IU pregnant mare serum (Folligon; Intervet, Dublin, Ireland), followed two days later by 5 IU human chorionic gonadotropin (hCG) (Chorulon; Intervet, Dublin, Ireland). The following day the animals were killed and uteri removed.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the RNeasy mini kit (Qiagen, Hilden, Germany) and quality measured with the Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA). Ten nanograms of high-quality RNA (RIN>8) was used for RNA-seq.
One 46-plex STRT RNA-seq library was made using 10 ng RNA as described previously (Krjutskov et al. 2016 Hum Reprod 31:844) with the following modifications: barcoded 10 µM template-switching oligonucleotides were added prior to reverse transcriptase, ERCC spike-in Mix A was diluted 15,300-fold with clean water, and 1 µl was taken per library reverse transcriptase master mix. Twenty cycles of PCR were used for the first round of amplification and ten additional cycles for the second round to introduce Illumina-compatible universal sequences.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
E8
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| Data processing |
The libraries were sequenced by two lanes of Illumina HiSeq2000 instrument. The sequenced raw STRT reads were processed by STRTprep [PMID: 26874359]; v3dev branch, d7efcde commit (https://github.com/shka/STRTprep/tree/v3dev) to demultiplex according to the barcode, and to exclude redundant reads according to the UMI; sequence of the template switching oligo (UMI, barcode and tri-G) were trimmed.
A gft file comprising annotations retrieved from UCSC and the ERCC annotations, was used to estimate the reads in all annotated genes using htseq-count.
Genome_build: Mm9
Supplementary_files_format_and_content: Tab delimited text file with raw gene counts of annotated genes and ERCC controls
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| Submission date |
Feb 23, 2018 |
| Last update date |
Jun 20, 2019 |
| Contact name |
Pauliina Damdimopoulou |
| E-mail(s) |
pauliina.damdimopoulou@ki.se
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| Organization name |
Karolinska Institute
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| Street address |
Karolinska University Hospital OBGY K57
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| City |
Stockholm |
| ZIP/Postal code |
14186 |
| Country |
Sweden |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE111035 |
Maternal Plag1 deficiency delays two-cell stage embryo development and embryonic genome activation [Uterus] |
| GSE111040 |
Maternal Plag1 deficiency delays two-cell stage embryo development and embryonic genome activation |
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| Relations |
| BioSample |
SAMN08583689 |
| SRA |
SRX3736979 |
| 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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