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| Status |
Public on Sep 02, 2015 |
| Title |
Mixed Tissue for pineal/mixed comparison |
| Sample type |
SRA |
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| Source name |
mixed-tissue
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
experiment type: in-vivo
tissue: mixed-tissue
time-point: Day
surgical condition: NA
treatment condition: NA
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| Treatment protocol |
Other than the 3 samples for the pineal/mixed-tissue comparison, all conditions had 3 biological replicates. For the in-vivo data, there were 8 biological conditions: two time points (Day and Night) for each of four surgical groups: Control (Ctrl) Sham-surgery (Sham), Decentralized (DCN), and Ganglionectomized (SCGX). For the in-vitro data there were 3 biological conditions: Untreated control (CN), DBcAMP-treated (DB), and Norepinephrine-treated (NE). Additionally, 3 samples were used to compare pineal tissue to mixed tissue: Pineal-Day (SD1), Pineal-Night (SN2), and Mixed-Tissue (SS3).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol reagent (Invitrogen, Carlsbad, CA), followed by clean-up using an RNeasy Micro Kit with on-column DNase treatment as per the manufacture’s protocol (Qiagen, Valencia, CA). The amount and quality of RNA were determined using a NanoDrop spectrophotometer (NanoDrop, Wilmington, DE) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Each pool yielded 2.1 to 3.7 micrograms of total RNA (RIN values > 9).
Stranded RNA-seq libraries were constructed from 0.7-1 µg total RNA using the TruSeq Stranded Total RNA Sample Prep Kits (Illumina cat. no. RS-122-2301) according to manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Initial processing (base calling, etc) by RTA version 1.17.21.3 and CASAVA 1.8.2
Alignment via RNA-STAR v2.3.1y, using the Ensembl RGSC3.4.69 transcript annotation
Quality control checks and gene counts via QoRTs, v0.0.23, using the Ensembl RGSC3.4.69 transcript annotation, "union" rule
Differential Expression analysis via DESeq2, R version 3.0.2, DESeq2 version 1.2.10
Genome_build: rn4
Supplementary_files_format_and_content: Tab delimited read-pair counts for each sample, generated via QoRTs. These use the "union" rule, and the methods are identical to those implemented by HTSeq.
Supplementary_files_format_and_content: tab delimited RPKM counts for each sample, calculated from the read counts. NOTE: these values are actual read pair counts per million, per kilobase, not estimates of RPKM generated using a more-advanced normalization method. For most purposes, raw counts and/or geometric or TMM normalization should be used for comparisons between samples.
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| Submission date |
Nov 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen William Hartley |
| E-mail(s) |
[email protected]
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| Phone |
301-451-0277
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| Organization name |
NHGRI, NIH
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| Department |
Cancer Genetics and Comparative Genomics Branch
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| Lab |
Comparative Genomics Analysis Unit
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| Street address |
5625 Fishers Lane
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| City |
Rockville |
| State/province |
MD |
| ZIP/Postal code |
20850 |
| Country |
USA |
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| Platform ID |
GPL14844 |
| Series (1) |
| GSE63309 |
RNA-Seq of the rat pineal transcriptome, with in-vivo and in-vitro samples, under various treatment and surgical conditions |
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| Relations |
| BioSample |
SAMN03195729 |
| SRA |
SRX759843 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1545534_RPKM_SS3.txt.gz |
264.3 Kb |
(ftp)(http) |
TXT |
| GSM1545534_readPairCounts_SS3.txt.gz |
122.1 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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