|
| Status |
Public on Mar 12, 2014 |
| Title |
Control littermates (n=3) |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow nestin+ cells, control
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: Nes-gfp
cell type: bone marrow CD45- CD31- Ter119- Nes-GFP+ cells
developmental stage: adult
|
| Treatment protocol |
pIpC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was obtained using Picopure RNA isolation kit (Arcturus).
cDNA Amplification: Amplified cDNAs were prepared from RNA samples (2-3 ng) using Ovation RNA-SeqSystem v2 (Nugen).
Library preparation: 1 ug of amplified cDNAs were fragmented by sonication to an average size of 300 pb aprox. Libraries for high-throughput sequencing were prepared from fragmented cDNAs using the Truseq DNA Sample Prep Kit (Illumina).
Sequencing: Libraries were sequenced in a Genome Analyzer IIx using standard procedures.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Control
|
| Data processing |
Fastq files obtained and demultiplexed with CASAVA1.8.
Illumina adaptors were trimmed with cutadapt v1.2.1.
First 15 nucleotides were trimmed with fastx_timmer to remove signatures left by ovation protocol.
PolyGC stretches at the beginning of the reads were also removed.
Reads shorter than 30nt were discarded for posterior analysis.
Reads were mapped with tophat v2.0.7 and bowtie 2.0.6.
Gene FPKM were quantified using Cufflinks.
Gene build: Ensembl v70
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKMs
|
| |
|
| Submission date |
Mar 11, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Simón Méndez-Ferrer |
| E-mail(s) |
smendez@cnic.es
|
| Organization name |
CNIC
|
| Lab |
Stem cell niche pathophysiology
|
| Street address |
Calle Melchor Fernández Almagro, 3
|
| City |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE55798 |
Neuropathy of the haematopoietic stem cell niche is essential for myeloproliferative neoplasms [RNA-seq] |
| GSE55802 |
Neuropathy of haematopoietic stem cell niche is essential for myeloproliferative neoplasms |
|
| Relations |
| BioSample |
SAMN02687927 |
| SRA |
SRX484660 |
