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| Status |
Public on Apr 21, 2019 |
| Title |
AMC4_RNAseq |
| Sample type |
SRA |
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| Source name |
hypothalamus
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: hypothalamus
gender: Male
age: postnatal day 9
treatment: augmented maternal care
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| Extracted molecule |
total RNA |
| Extraction protocol |
Extracted and purified using the Qiagen RNeasy kit
Total RNA was isolated from AMC and control hypothalamus using the RNeasy Kit (Qiagen, Valencia, CA). Total RNA samples were then processed with a Gene Read ribosomal RNA depletion kit (Qiagen, Germantown PA) prior to Illumina Hi-Seq library preparation using a directional RNA-seq library kit (NEB, Ipswich, MA). Libraries were checked by Bioanalyzer analysis (Agilent, Santa Clara, CA) for quality, then 50 base pair, single end reads were acquired on a Hi-Seq 2500 (Illumina, San Diego, CA) at the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkley.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Post-mortem brain
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| Data processing |
The Hi-Seq 2500 reads were trimmed using Trimmomatic and Illuminaclip single end adapter trimming
final quality was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
RNA-seq reads were aligned to the current UCSC rat genome rn6 using the splicing-aware aligner Tophat2 (v2.0.14, stranded, Single End).
Differential expression was analyzed using cufflinks (v2.2.1) with bias, multi-read, and length corrections.
Cuffdiff was performed using a Cuffmerge generated gtf from all assembled transcripts and RefSeq UCSC genes using a genometric pooled dispersion model and minimum alignment of 10 fragments.
Genome_build: rn6
Supplementary_files_format_and_content: Strand specific RNAseq bigwig showing read coverage over the genome
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| Submission date |
May 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Keith Dunaway |
| E-mail(s) |
kwdunaway@ucdavis.edu
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| Organization name |
UC Davis
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| Department |
MMI
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| Lab |
LaSalle Lab
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| Street address |
3318 Tupper Hall
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (2) |
| GSE99278 |
Integrative epigenomic analyses of early-life hypothalamic response to augmented maternal care [RNA-seq] |
| GSE99282 |
Integrative epigenomic analyses of early-life hypothalamic response to augmented maternal care |
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| Relations |
| BioSample |
SAMN07163654 |
| SRA |
SRX2851952 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2640297_JLDY109A_neg_strand.bigwig |
56.1 Mb |
(ftp)(http) |
BIGWIG |
| GSM2640297_JLDY109A_pos_strand.bigwig |
56.5 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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