|
| Status |
Public on Nov 03, 2022 |
| Title |
s-E15.5-GNTHOM-4 |
| Sample type |
SRA |
| |
|
| Source name |
mouse E15.5 embryos
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Dicer GNT/GNT
age: E15.5
tissue: embryo
fraction: small RNA
replicate: 3
|
| Treatment protocol |
E15.5 embryos were removed from the uterus and washed in PBS. The yolk sac was taken for genotyping and embryos were transferred into RNAlater (Thermo Fisher Scientific)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryos were homogenized in Qiazol lysis reagent (Qiagen) and total RNA was isolated by Qiazol-chloroform extraction and ethanol precipitation method.
Small RNA libraries were constructed using Nextflex Small RNA-seq kit v3 for Illumina (Perkin Elmer) according to the manufacturer’s protocol; 3′ adapter ligation was performed overnight at 20 °C, 15 cycles were used for PCR amplification and NextFlex beads were used for size selection.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Small RNA-seq reads were trimmed using fastx 0.0.14 and cutadapt 1.8.3: zcat ${FILE}.fastq.gz | fastx_trimmer -f 5 -i - -o ${FILE}.tmp.fastq cutadapt --format="fastq" --front=GTTCAGAGTTCTACAGTCCGACGATCNNNN --adapter=NNNNTGGAATTCTCGGGTGCCAAGG --error-rate=0.075 --times=2 --overlap=14 --minimum-length=12 --max-n=0.1 --output="${FILE}.fastq" --trim-n --match-read-wildcards ${FILE}.tmp.fastq
Trimmed reads were mapped to mouse (mm10) genome using STAR 2.7.3a with following parameters: STAR --readFilesIn ${FILE}.fastq.gz --genomeDir ${GENOME_INDEX} --runThreadN 12 --genomeLoad NoSharedMemory --limitBAMsortRAM 20000000000 --readFilesCommand unpigz –c --outFileNamePrefix ${FILENAME} --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMultimapNmax 99999 --outFilterMismatchNoverLmax 0.1 --outFilterMatchNminOverLread 0.66 --alignSJoverhangMin 999 --alignSJDBoverhangMin 999
Genome browser coverage tracks in bigWig format were produced using bedtools v2.29.2 and wigToBigWig v 4 from UCSC: genomeCoverageBed -ibam ${FILE} -bg -split > ${FILE}.bedGraph wigToBigWig ${FILE}.bedGraph chrNameLength.txt ${FILE}.bw
Genome_build: mm10
Supplementary_files_format_and_content: coverage genome browser tracks files: - .bigWig format - generated in a non-stranded mode. - not normalized for library size
|
| |
|
| Submission date |
Feb 07, 2022 |
| Last update date |
Nov 03, 2022 |
| Contact name |
Filip Horvat |
| E-mail(s) |
filip.horvat@img.cas.cz
|
| Organization name |
Institute of Molecular Genetics of the ASCR
|
| Lab |
Laboratory of Epigenetic Regulations
|
| Street address |
Videnska 1083
|
| City |
Prague |
| ZIP/Postal code |
14220 |
| Country |
Czech Republic |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE196305 |
The helicase domain of Dicer ensures essential accuracy of miRNA biogenesis in mice |
| GSE196310 |
The helicase domain of Dicer ensures essential accuracy of miRNA biogenesis in mice |
|
| Relations |
| BioSample |
SAMN25716693 |
| SRA |
SRX14077131 |
