|
| Status |
Public on Jul 19, 2018 |
| Title |
iRx_noDox_RNAseq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
un-induced RNA-seq
|
| Organism |
Mus musculus |
| Characteristics |
mouse strain: 129P2/OlaHsd
cell type: haemogenic endothelium (HE) cells
genotype: un-induced
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cells using TRIzol (Invitrogen) according to manufacturer’s instructions. First-strand cDNA synthesis was carried out using Superscript II (Invitrogen) and Oligo dT (Invitrogen) according to manufacturer’s instructions. RNA was DNase treated using Turbo DNase (Ambion) and a further clean-up step was performed using the RNA Nucleospin kit (Macherey-Nagel) according to manufacturer’s instructions. Real-time PCR was carried out using Applied Biosystems SYBR green master mix (Thermo Fisher) with 5 μl of diluted cDNA and 0.25 μM forward and reverse primers per 10 μl reaction on an ABI 7900HT machine. Analysis was carried out on samples measured in duplicate.
RNA-seq libraries were prepared using the Tru-seq Stranded Total RNA kit (Illumina), according to manufacturer’s instructions. Libraries were sequenced in a pool of 12 indexed libraries using a NextSeq® 500/550 High Output Kit v2 (150 cycles) for paired end sequencing (Illumina, FC-404-2002) at the Genomics Birmingham sequencing facility.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Quality of reads was verified using FASTQC analysis
RNA-Seq reads were aligned to the mm10 mouse genome build using STAR.
Separate density files for the positive and negative strand were generated for RNA-seq data and uploaded to the UCSC genome browser
Fragments per Kilobase of transcript per Million mapped reads (FPKM) values for each gene were extracted using Cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph
|
| |
|
| Submission date |
Sep 20, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Salam Adli Assi |
| E-mail(s) |
s.a.assi@bham.ac.uk
|
| Organization name |
University of Birmingham
|
| Department |
Institute for Cancer and Genomic Sciences
|
| Street address |
IBR
|
| City |
Birmingham |
| ZIP/Postal code |
B15 2TT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE104044 |
System-wide Dissection of the Transcriptional Response to RUNX1 During Hematopoietic Specification [RNA-seq] |
| GSE104046 |
The Co-operation of RUNX1 with LDB1, CDK9 and BRD4 Drives Transcription Factor Complex Relocation During Haematopoietic Specification |
|
| Relations |
| BioSample |
SAMN07674690 |
| SRA |
SRX3200426 |
