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| Status |
Public on Apr 06, 2021 |
| Title |
Fosl1_30B |
| Sample type |
SRA |
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| Source name |
NMUMG cells, clone E9
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| Organism |
Mus musculus |
| Characteristics |
tissue: NMUMG cells, clone E9
tgfb treatment: 4d
sirna transfected: siFosl1
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the miRNeasy Mini Kit (Qiagen). 1µg total RNA was electrophoresed to isolate the miRNA fraction from 17 to 29 nct. After extraction from the PAGE gel and precipitation, RNA was resuspended in 4ul Rnase-free water
MicroRNAs were ligated with 3’ adapters, RT primers annealed, then 5' adapters ligated followed by reverse transcription and amplification including one of 48 different reverse primers. The amplified cDNA constructs were gel purified using QIAEX II Gel Extraction Kit (Qiagen) and eluted in 25µl water. Libraries were quality-checked on the Fragment Analyzer and samples pooled by batches of of 48, 40 and 42 libraries respectively in equal molarity. Each pool was further quantified with Pico-Green. 11pM and used for clustering on the cBot2 (Illumina). Samples were sequenced Single-Read over 51 cycles on HiSeq2500 using the HiSeq Flow Cell v4 (Illumina) and the HiSeq SBS Kit v4 (Illumina). Primary data analysis was performed with the Illumina RTA version 1.18.64 and bcl2fastq-2.16.0.10.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Sequencing adapters were removed from obtained single-end miRNA-seq reads (51-mers).
Preprocessed reads were mapped to mouse genome assembly, version mm10, with Bowtie (included in R/Bioconductor package QuasR, version 1.0.9.) allowing up 50 hits in the genome.
miRNA coordinates from miRBase (http://www.mirbase.org/, version 21) were extented by 3bp on each side and miRNA expression levels were quantified as the number of reads that started within any extended mature miRNA.
The differentially expressed miRNAs were identified using the edgeR package (version 3.2.4).
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw counts for miRNAs, 1.column is miRNA id, 2. and remaining columns contain raw counts
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| Submission date |
Apr 12, 2018 |
| Last update date |
Nov 17, 2021 |
| Contact name |
DBM Bioinformatics Core Facility |
| Phone |
+41612073541
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| Organization name |
University of Basel
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| Department |
Departement of Biomedicine
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| Street address |
Hebelstrasse 20
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| City |
Basel |
| State/province |
BS |
| ZIP/Postal code |
4053 |
| Country |
Switzerland |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE113038 |
Transcription (co)factor and miRNA regulatory landscape of EMT (miRNA-seq) |
| GSE115376 |
Transcription (co)factor and miRNA regulatory landscape of EMT |
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| Relations |
| BioSample |
SAMN08918539 |
| SRA |
SRX3927106 |
| 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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