|
| Status |
Public on Sep 16, 2020 |
| Title |
STRAP Embryo eCLIP Input |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Mus musculus |
| Characteristics |
tissue: embryo
strain: C57BL/6
age: prenatal day 9.5
genotype: wild type
|
| Growth protocol |
EB cells were cultured in ES medium without LIF and then cultured in N2B27 medium supplemented with 10ng/ml bFGF for additional 5 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
UV-crosslinked EBs or embryos were lysed in CLIP lysis buffer followed by sonication and STRAP-RNA complexes were isolated with anti-STRAP antibody.
eCLIP libraries were prepared for sequencing using eCLIP-seq protocols.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Library strategy: eCLIP-seq
Basecalls performed using Illumina's bcl2fastq version 2.18.0.12
Cutadapt version was used to trim primer adapters from raw FASTQ files using parameters: -f fastq --match-read-wildcards --times 1 -e 0.1 -O 1 --quality-cutoff 6 -m 18 -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT
To remove repetive elements, STAR version 2.5.2b was used on the trimmed FASTQ files using paramters: --outSAMunmapped Within --outFilterMultimapNmax 30 --outFilterMultimapScoreRange 1 --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline $RG --alignEndsType EndToEnd
The unmapped reads from the first STAR alignments were then mapped to mm10 using STAR version 2.5.2b using parameters: --outSAMunmapped Within --outFilterMultimapNmax 30 --outFilterMultimapScoreRange 1 --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --alignEndsType EndToEnd
Peaks were called on mm10 alignments using MACS version 1.4.2 using parameters: -t -c --name --format="BAM" -g mm --tsize=75
Genome_build: GRCm38 p4 Release M11
Supplementary_files_format_and_content: Tab-delimited Excel file containing the peaks identified for each sample by MACS
|
| |
|
| Submission date |
May 20, 2019 |
| Last update date |
Sep 18, 2020 |
| Contact name |
Pran K Datta |
| E-mail(s) |
prandatta@uabmc.edu
|
| Phone |
2059756039
|
| Organization name |
University of Alabama at Birmingham
|
| Department |
Medicine
|
| Lab |
WTI 530
|
| Street address |
1824 6th Ave South, WTI 520C
|
| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE131472 |
Transcriptome-wide maps of STRAP-RNA interactions in mouse early embryo and lineage-committed cells. |
| GSE131474 |
STRAP-dependent alternative splicing events; STRAP-RNA interactions in mouse early embryo and lineage-committed cells. |
|
| Relations |
| BioSample |
SAMN11784078 |
| SRA |
SRX5865851 |
