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| Status |
Public on Mar 06, 2024 |
| Title |
E13.5_Mammary_Mes_rep2 |
| Sample type |
SRA |
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| Source name |
E13.5 Mammary mesenchyme
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| Organism |
Mus musculus |
| Characteristics |
tissue: E13.5 Mammary mesenchyme
developmental stage: E13.5
strain: C57Bl/6JOlaHsd
Sex: not applicable
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| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were lysed immediately after collection and stored in TRI Reagent (T9424, Sigma) at -80 °C. Total RNA was extracted using Direct-zol RNA Microprep kit (Zymo Research, Irvine, CA) with DNase treatment according to the manufacturer's instructions. RNA quality was assessed with 2100 Bioanalyzer (Agilent, Santa Clara, CA) using Agilent RNA 6000 Pico Kit or Agilent RNA 6000 Nano Kit (Agilent, Santa Clara, CA). RNA concentration was determined using Qubit RNA HS Assay Kit (Q32855, Thermo Fisher) with Qubit 4 Fluorometer (Thermo Fisher).
cDNA libraries were prepared with Ovation SoLo RNA-seq System (NuGen/Tecan Genomics) according to manufacturer's instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Sample_113
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| Data processing |
All sequencing reads were processed for quality control, removal of low-quality reads, adaptor sequence and ribosomal RNA using fastqc version 0.11.8 , multiqc version 1.9 , Trimmomatic version 0.39 and SortMeRNA version 2.1 accordingly.
The filtered reads were mapped to the reference genome (mm10) using Salmon version 0.99.0
Read counts were extracted and normlized using tximport (1.15.10) and DESeq2 (3.15).
Assembly: mm10
Supplementary files format and content: tab separated, normalized counts file
Supplementary files format and content: rds file
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| Submission date |
Feb 22, 2023 |
| Last update date |
Mar 06, 2024 |
| Contact name |
Marja Mikkola |
| E-mail(s) |
marja.mikkola@helsinki.fi
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| Organization name |
University of Helsinki
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| Street address |
P.O.Box 56
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| City |
Helsinki |
| ZIP/Postal code |
00014 |
| Country |
Finland |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE225821 |
Identification of the mesenchymal signals regulating embryonic mammary gland development |
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| Relations |
| BioSample |
SAMN33415358 |
| SRA |
SRX19471600 |
| 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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