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Series GSE104051 Query DataSets for GSE104051
Status Public on Jun 14, 2019
Title AGO CLIP reveals an activated network for acute regulation of brain glutamate homeostasis in ischemic stroke [dataset 7]
Sample organism Mus musculus
Experiment type Third-party reanalysis
Expression profiling by high throughput sequencing
Summary In vivo microRNA-target interactions from adult mouse cortex were identified with CLEAR-CLIP, a modified AGO HITS-CLIP approach that allows direct ligation of microRNA and target within purified, endogenous AGO-RNA complexes.
 
Overall design Native AGO-RNA complexes were purified under stringent conditions selectively preserve cross-linked AGO-target interactions, then microRNA and target mRNA were ligated within the AGO complex to form miRNA-target chimeras in addition to standard AGO CLIP reads. AGO-bound RNAs were cloned by addition of a pre-adenylated 3' linker, a 5' RNA linker containing a 4 nt degenerate barcode followed by a G (NNNNG), and RT-PCR amplification. A second round of PCR amplification added a 4 nt index (for multiplexing) followed by a 16 nt common priming sequence. Raw data files have been de-multiplexed, but are otherwise not modified.
DATA PROCESSING: base calling: Casava 1.8.2 quality filtering: minimum quality filter applied for barcode and insert; fastq_filter.pl; -if sanger -f min:0-3:20,mean:20-40:20 -maxN -1 -v -of fasta ; http://sourceforge.net/projects/ngs-cims/files/CIMS.v1.0.5.tgz/download collapse exact sequences: exact duplicate sequences removed; fasta2collapse.pl; ; http://sourceforge.net/projects/ngs-cims/files/CIMS.v1.0.5.tgz/download remove 3' adapter sequene: 3' adapter GTGTCAGTCACTTCCAGCGG clipped; fastx Clipper; -l 20 -a GTGTCAGTCACTTCCAGCGG -n; http://hannonlab.cshl.edu/fastx_toolkit/ trim 5' adapter sequence: 5' 20 nucleotides trimmed (NNNNAGGGAGGACGATGCGG, where NNNN is 4 nucleotide index for multiplexing); fastx Trimmer; -f 21; http://hannonlab.cshl.edu/fastx_toolkit/ strip 5' degenerate linker: 5 nucleotide (NNNNG) degenerate barcode stripped and appended to read IDs; stripBarcode.pl; -linker 5 ; http://sourceforge.net/projects/ngs-cims/files/CIMS.v1.0.5.tgz/download alignment against micoRNA database: microRNA database mapped against sample file (treated as reference genome) to identify potential chimeric reads containing microRNA sequence; Bowtie; -n 1 -l 8 -e 35; http://bowtie-bio.sourceforge.net/index.shtml extract chimeric read: extract potential chimeric sequence 5' or 3' of mapped microRNA sequence; text manipulation in R; ; alignment against genome reference: alignment ofpotential chimeric reads against reference genome to identify target sites; Bowtie; -n 1 -l 8 -e 35; http://bowtie-bio.sourceforge.net/index.shtml collapse PCR duplicates: mapped reads with same 5' end and same degenerate barcode consolidated; tag2collapse.pl; keep-tag-name --keep-max-score --random-linker -EM 30 --seq-error-model em-local --weight --weight-in-name ; http://sourceforge.net/projects/ngs-cims/files/CIMS.v1.0.5.tgz/download clustering : chimera interactions with the same ligated microRNA and overlapping genomic coordinates were clustered; Genome_Intervals R package; ;
mm10 genomic coordinates of 126,295 CLEAR CLIP chimeras, chromosome, start, end, associated mmu miRNA, strand info
 
Contributor(s) Kobayashi M, Moore MJ
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Sep 20, 2017
Last update date Jun 14, 2019
Contact name Mariko Kobayashi
E-mail(s) mkobayashi@rockefeller.edu
Organization name Rockefeller University
Department Molecular Neuro-Oncology
Lab Robert B. Darnell
Street address 1230 York Avenue
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
This SubSeries is part of SuperSeries:
GSE104053 AGO CLIP reveals an activated network for acute regulation of brain glutamate homeostasis in ischemic stroke
Relations
Reanalysis of GSM1881539
Reanalysis of GSM1881540
Reanalysis of GSM1881541
BioProject PRJNA408122

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE104051_6wkcortex-CLEARCLIP_sites.txt.gz 1.1 Mb (ftp)(http) TXT
Processed data are available on Series record

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