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| Status |
Public on Sep 09, 2016 |
| Title |
18.5-1 |
| Sample type |
SRA |
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| Source name |
pancreas
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| Organism |
Mus musculus |
| Characteristics |
tissue: pancreas
strain: C57Bl/6
embryonic day: 18.5
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| Growth protocol |
timed matings. noon of day that sperm plug was detected was considered E0.5. Embryos were collected at noon on E18.5.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA preparation: pancreas was homogenized in 4 M Guanidine Thiocyanate, 0.1 M Tris HCl pH 7.5, 1% 2-mercaptoethanol with a Tekmar Tissuemizer. RNA was isolated from an aliquot of the homogenate by addition of N-Lauroylsarcosine sodium salt to 0.5%, Potassium Acetate pH 5.5 to 0.1 M, and Acetic Acid to 0.08 M, followed by addition of 0.75 volume ethanol while vortexing. RNA was allowed to precipitate from the solution at -20 C for at least 1 hour, collected by centrifugation at 12,000 g for 5', and the RNA pellet resuspended in Trizol (equal volume to starting homogenate). Subsequent steps were as per manufacturer's protocol (Life Technologies).
RNA libraries were prepared for sequencing using standard Illumina True-seq protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
total RNA RIN 8.8
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| Data processing |
Illumina HiSeq Control Software version 2.0.10.0 used for basecalling
Sequences were mapped to mm9 mouse genome using TopHat v2.0.4 (by use of Bowtie v0.12.7.0) with parameters --no-novel-juncs --segment -length 25 --segment-mismatches 3
Sequences per gene were counted using Samtools ( v0.1.18.0) /HTSeq (v0.6.0)
Counts-per-million (CPM) were calculated using TMM normalization according to Robinson et al., Bioinformatics, 2010. Data set was filtered for minimal expression by "keep <- rowSums(cpm(d)) >= 3"
Differential gene expression analysis was performed with edgeR v3.0.8 (FDR < 0.05)
Genome_build: mm9
Supplementary_files_format_and_content: Normalized counts-per-million (CPM) for each sample in tab-delimited text file
Supplementary_files_format_and_content: EdgeR results as .xlxs spreadsheets, comparison with Adult induced knockout samples GSM2299179 6d_cKO1, GSM2299180 6d_cKO2, GSM2299181 6d_cKO3 and control animals from this study GSM2299174 6d_CT1, GSM2299175 6d_CT2, GSM2299176 6d_CT3, GSM2299177 6d_CT4, GSM2299178 6d_CT5 and fdr < 0.05.
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| Submission date |
Sep 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Galvin Swift |
| E-mail(s) |
galvin.swift@utsouthwestern.edu
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| Organization name |
U TX Southwestern Medical Center
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| Department |
Molecular Biology
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| Lab |
Ray MacDonald
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| Street address |
6000 Harry Hines Blvd
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| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-9148 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE86263 |
Transcriptional Maintenance of Pancreatic Acinar Identity, Differentiation and Homeostasis by PTF1A |
| GSE86568 |
Transcriptional Maintenance of Pancreatic Acinar Identity, Differentiation and Homeostasis by PTF1A [E18.5 RNA-Seq] |
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| Relations |
| BioSample |
SAMN05751625 |
| SRA |
SRX2148078 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2305985_Htseq_lane8_Swift_59067-1_1_e18-5.txt.gz |
97.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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