|
Status |
Public on Jan 03, 2017 |
Title |
SC-8 |
Sample type |
SRA |
|
|
Source name |
human fetus
|
Organism |
Homo sapiens |
Characteristics |
cell type: NA fetal region: Spinal Cord embryonic age: 11 weeks antibody: none
|
Treatment protocol |
none
|
Growth protocol |
none
|
Extracted molecule |
polyA RNA |
Extraction protocol |
miRNeasy Micro Kit (Qiagen) KAPA stranded RNA-seq with RiboErase kit.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 3000 |
|
|
Description |
Processed data in Embryo.Repeats.uniqID.UniqueReads.NOT.IN.EXON.final.txt
|
Data processing |
RNA-seq reads were mapped to the human genome assembly hg38 using STAR aligner v4.1. For mRNA analysis, default parameters were used. For analysis of retrotransposons we used the --outFilterMultimapNmax 1 to only report uniquely mapping reads ChIP-seq reads were mapped to the human genome assembly hg38 using Bowtie2 with --very-sensitive. All alignments with MAPQ < 10 were discarded. ChIP-seq peaks were called with MACS2 normalizing against IN. H3K9me3 peaks were called using --broad, TRIM28 peaks were called with default parameters. A cutoff of -q 0.05 was used for both data sets. mRNA and non-coding RNAs were quantified using the subread package FeatureCounts (--primary) and iGenome NCBI annotation. Retrotransposons were quantified using the RepeatMasker track from UCSC. Genome_build: hg38 Supplementary_files_format_and_content: RNA-Seq: Matrix of quantification of non-exonic retroelements using featureCounts. Supplementary_files_format_and_content: ChIP-Seq: Bed files with called peaks.
|
|
|
Submission date |
Jul 11, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Per Brattas |
Organization name |
Lund University
|
Lab |
Clinical Genomics
|
Street address |
Sölvegatan 17
|
City |
Lund |
ZIP/Postal code |
221 84 |
Country |
Sweden |
|
|
Platform ID |
GPL21290 |
Series (1) |
GSE84259 |
TRIM28 controls a gene regulatory network based on endogenous retroviruses in human neural progenitor cells |
|
Relations |
BioSample |
SAMN05372142 |
SRA |
SRX1925747 |