|
| Status |
Public on Sep 26, 2016 |
| Title |
E11.5 LMPP_replicate3 |
| Sample type |
SRA |
| |
|
| Source name |
E11.5 Fetal liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: E11.5 Fetal liver
strain: C57 BL6, Rag1-GFP reporter mouse
phenotype: Lin-c-Kit+Flt3+IL-7Ralpha+
|
| Treatment protocol |
Cell populations isolated by FACS sorting
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
cDNA was generated as described in the manual for "SMARTer Ultra Low RNA Kit for Illumina sequencing" marketed by Clontech. Then, a sequencing library was generated as described in Illumina's "Ultra Low Input mRNA-Seq Guide".
For RNA-Seq NEBNext® DNA Library Prep Reagent Set for Illumina®
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-Seq: Reads were aligned using Bowtie against the murine transcriptome (mouse NCBI build37 Refseq transcripts)
RNA-Seq: Non-uniquely mapped reads were discarded. Count number of reads for each transcript and reads per kilobase of a transcript per million mapped reads (RPKMs) were calculated and assigned to each transcript.
RNA-Seq: Overlapping Refseq transcripts were collapsed giving the highest one expression value per gene loci.
RNA-Seq: Gene expression levels for Refseq genes were summarized as reads per kilobase of exon model per million mapped reads (RPKM) and read counts using custom R scripts
Genome_build: mm9
Supplementary_files_format_and_content: Read counts and RPKM values from RNA sequencing
|
| |
|
| Submission date |
Dec 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Claus Nerlov |
| E-mail(s) |
claus.nerlov@imm.ox.ac.uk
|
| Organization name |
Weatheral Institute of Molecular Medicine
|
| Department |
MRC Molecular Haematology Unit
|
| Lab |
Nerlov Laboratory
|
| Street address |
John Radcliffe Hospital, University of Oxford
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE76140 |
Initial seeding of the embryonic thymus by an immune-restricted lympho-myeloid progenitor independently of Notch signaling |
|
| Relations |
| BioSample |
SAMN04349984 |
| SRA |
SRX1490909 |
