|
| Status |
Public on Dec 06, 2016 |
| Title |
Het_RNA_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Het_RNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
cell type: embryonic stem cell (ESC)
genotype/variation: EZH2 -/+ (Het)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Human ESC were isolated by FACS straight into TRIzol LS (Life Technologies). Total RNA was purified and then cleaned up using an RNeasy kit (Qiagen).
Indexed mRNA-Seq libraries were constructed from 500ng total RNA using the Tru-Seq RNA Library Prep Kit v2 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNA-Seq_RPM.txt
|
| Data processing |
RNA-Seq reads were trimmed using Trim Galore v0.4.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence. They were mapped to the human GRCh38 genome assembly using Tophat 2.0.12 guided by the gene models from the Ensembl v70 release. BAM files were imported into Seqmonk v32.1 (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). Raw read counts per transcript were calculated using the RNA-Seq quantitation pipeline on the Ensembl v70 gene set using non-directional counts.
Processed data files format and content: Quantitated RNA-Seq data file is tab delimited and contains the following columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) mRNA ID (Ensembl) (7) Description (Ensembl); (8-19) log2 RPM value
Libraries were sequenced on the Illumina HiSeq1000/2500 platforms using the default RTA analysis software.
Genome_build: GRCh38
|
| |
|
| Submission date |
Jan 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Felix Krueger |
| E-mail(s) |
fkrueger@altoslabs.com
|
| Organization name |
Altos Labs
|
| Department |
Bioinformatics
|
| Street address |
Granta Park
|
| City |
Cambridge |
| ZIP/Postal code |
CB21 6GP |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE76626 |
Characterization of EZH2-deficient human embryonic stem cells [ChIP-seq and bulk RNA-seq] |
| GSE81674 |
Characterisation of EZH2-deficient human embryonic stem cells |
|
| Relations |
| BioSample |
SAMN04388045 |
| SRA |
SRX1521202 |
