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| Status |
Public on Sep 11, 2013 |
| Title |
dorsal pancreas, E10.5 |
| Sample type |
SRA |
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| Source name |
dorsal pancreas, E10.5
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: dorsal pancreas
age: E10.5
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA sequencing was performed using approximately 20 – 70 ng total RNA quantified by Agilent RNA 6000 Pico Kit (Agilent Technologies). Briefly, poly (A) RNA was isolated by two rounds of Oligo (dT)25 Dynabeads (Invitrogen) purification. Purified poly (A) RNA was fragmented at 94 oC for 3.5 minutes using 5 x fragmentation buffer (200 mM Tris-Acetate, pH 8.1, 500 mM KOAc, 150 mM MgOA), as previously described [Adamidi C, 2011; PMID: 21536722]. The fragmented RNA was purified by Agencourt RNAClean XP SPRI beads (Agencourt) and converted to first strand cDNA using random hexamer primers (Invitrogen) and SuperScript II Reverse Transcriptase (Invitrogen), followed by second strand cDNA synthesis with E.coli DNA pol I (Invitrogen) and RNAse H (Invitrogen) according to the manufacturer’s manuals. Then the paired-end sequencing library was prepared using NEBNext DNA Library Prep. Kit (NEB) following the Illumina mRNA-Seq library preparation protocol (Illumina). The prepared sequencing library was subsequently sequenced on Illumina HiSeq for 2 x 100 cycles following the standard protocol (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
q5_FPKM
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| Data processing |
reads were mapped to reference genome mm9 using TopHat (v 1.33) with paramaters: -a 8 -m 1 -i 40 -I 1000000 -F 0 --solexa1.3-quals -p 4 -r 150 --coverage-search --keep-tmp -z /bin/gzip --no-convert-bam
transcript assembly and differential expression were determined using Cufflinks (v 1.3.0) with UCSC reference annotation
a set of 14053 non-redundant Cufflinks genes was obtained by filtering for: 1) successful deconvolution of FPKM; 2) FPKM> 0 in a least 2 samples; 3) lower confidence level of FPKM > 0 in at least two samples; 4) in the case that multiple Cufflinks genes for one gene symbol existed, Cufflinks genes were further selected for the longest transcript length and the highest variability in the FPKM across all samples
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file contains FPKM values for non-redundant set of transcripts (14053 genes) in all 5 samples
Read statistics: number of raw paired-end reads: 104526851; number of mapped paired-end reads: 99464506; number of uniquely mapped paired-end reads: 92694571
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| Submission date |
Sep 12, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Francesca M. Spagnoli |
| E-mail(s) |
francesca.spagnoli@kcl.ac.uk
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| Organization name |
King's College London
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| Department |
CGTRM
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| Lab |
Molecular and Cellular Basis of Embryonic Development
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| Street address |
Great Maze Pond
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| City |
London |
| ZIP/Postal code |
SE1 9RT |
| Country |
United Kingdom |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE40823 |
RNA-Seq profiling unveils a non-canonical Wnt signalling signature in pancreas versus liver fate decision |
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| Relations |
| SRA |
SRX186178 |
| BioSample |
SAMN01166112 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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