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Sample GSM2850629

Query DataSets for GSM2850629

Status

Public on Jan 23, 2019

Title

Glioblastoma_AGO2RIP_B9_totalRNA

Sample type

SRA

Source name

brain

Organism

Homo sapiens

Characteristics

tissue: Glioblastoma
rip antibody: anti-Ago2-3148
ago protein: AGO2

Extracted molecule

total RNA

Extraction protocol

Brain biopsies were lysed using TissueLyser LT and Immunoprecipitation was conducted using antibodies against AGO2. RNA extraction was done using the miRNAeasey mico kit.
NuGen Ovation RNAseq V2 kit, followed by the Ovation® Ultralow V2 Library or Ovation® Rapid Library Systems

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

featC.3UTR.txt.gz [3utr]
featC.linc.txt.gz [linc]
featC.refseq.txt.gz [refseq]
featC.RNR.txt.gz [RNR]
B9
total RNA seq

Data processing

Adaptors were trimmed using Cutadapt and qualtiy of reads were checked using FASTQC
Data was aligned either to the human (hg38) or to the mouse (mm10) genome using StarAligner 2.5.0a.
For analysis of small RNAs 1 mismatch per 22nt were allowed, for mRNA analyses default setting were used.
For the analyses of small RNAs deriving from transposable elements, we uniquely aligned the data to the human genome (hg38) using StarAligner 2.5.0a (0 mismatches). For the analysis of transposable elements in total RNA samples data was uniquely aligned, allowing for 2 mismatches in 50bp (--outFilterMismatchNoverLmax 0.04).
mRNA and non-coding RNAs were quantified using the subread package FeatureCoutns (primary reads) using annotation files from Ensembl and iGenomes NCBI annotations. Transposable elements were quantified using the RepeatMasker Track from UCSC.
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: featC.3UTR.txt.gz [Tab-delimited table with quantification of reads mapping to 3UTR annotation of Ensembl. Column 1-7 contains transcriptID,chr,start,end,strand and length. All other columns shows read numbers in each sample, identified in header]
featC.linc.txt.gz [Tab-delimited table with quantification of reads mapping to lncRNA annotation of NCBI igenomes. Column 1-7 contains transcriptID,chr,start,end,strand and length. All other columns shows read numbers in each sample, identified in header]
featC.refseq.txt.gz [Tab-delimited table with quantification of reads mapping to igenomes NCBI annotation. Column 1-7 contains transcriptID,chr,start,end,strand and length. All other columns shows read numbers in each sample, identified in header]
featC.RNR.txt.gz [Tab-delimited table with quantification of reads mapping to RNR from NCBI annotation. Column 1-7 contains transcriptID,chr,start,end,strand and length. All other columns shows read numbers in each sample, identified in header]
featC.repeatsONLYminOverlap.txt.gz [Tab-delimited table with quantification of reads mapping to repeats from UCSC genome browser RepeatMasker track annotations. Column 1: RepName, Column2: Total length of all elements of the given element subfamily. Column 3-: each column correspond to one sample, identified in header]
featC.repeatsONLYminOverlap2024.txt.gz [Tab-delimited table with quantification of 20-24 nt long reads mapping to repeats from UCSC genome browser RepeatMasker track annotation. Column 1: RepName, Column2: Total length of all elements of the given element subfamily. ]
featC.piRNA2024minOverlap.txt.gz [Tab-delimited table with quantification of 20-24 nt long reads mapping to piRNAs from piRNAbank annotations. Column 1-6 contains transcriptID,chr,start,end,strand and transcript length. Column 7-All other columns shows read numbers in each sample, identified in header]
featC.piRNAminOverlap.txt.gz [Tab-delimited table with quantification of reads mapping to piRNAs from piRNAbank annotations. Column 1-6 contains transcriptID,chr,start,end,strand and transcript length. Column 7-All other columns shows read numbers in each sample, identified in header]
featC.miRbaseminoverlap.txt.gz [Tab-delimited table with quantification of reads mapping to miRNAs from miRbase annotations. Column 1-6 contains transcriptID,chr,start,end,strand and transcript length. Column 7-All other columns shows read numbers in each sample, identified in header]
featC.miRbase2024_minoverlap.txt.gz [Tab-delimited table with quantification of 20-24nt long reads mapping to miRNAs from miRbase annotations. Column 1-6 contains transcriptID,chr,start,end,strand and transcript length. Column 7-All other columns shows read numbers in each sample, identified in header]
featC.hg38tRNA_minO.txt.gz [Tab-delimited table with quantification of reads mapping to tRNAs from UCSC genome browser RepeatMasker track annotations. Column 1-6 contains transcriptID,chr,start,end,strand and transcript length. Column 7-All other columns shows read numbers in each sample, identified in header]
featC.small.hg38tRNAminO.txt.gz [Tab-delimited table with quantification of 20-24nt reads mapping to tRNAs from UCSC genome browser RepeatMasker track annotations. Column 1-6 contains transcriptID,chr,start,end,strand and transcript length. Column 7-All other columns shows read numbers in each sample, identified in header]
featC.3UTRCells.txt.gz [Tab-delimited table with quantification of reads mapping to 3UTR annotation of Ensembl. Column 1 contains transcriptID. Column 2: reads of RIP and input samples]
Bigwigs

Submission date

Nov 13, 2017

Last update date

May 15, 2019

Contact name

Per Brattas

Organization name

Lund University

Lab

Clinical Genomics

Street address

Sölvegatan 17