|
Status |
Public on Sep 16, 2020 |
Title |
STRAP Embryo eCLIP-2 |
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 |
SAMN11784077 |
SRA |
SRX5865852 |