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| Status |
Public on Feb 06, 2020 |
| Title |
AGA CON rep 4 |
| Sample type |
SRA |
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| Source name |
hippocampus
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| Organism |
Sus scrofa |
| Characteristics |
breed: PIC Camborough (dam) x PIC 359 (sire)
tissue: brain
age: post natal day 14
size: AGA
diet: CON
Sex: F
pair: 8
cohort: 2
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| Treatment protocol |
Hippocampi were dissected and stabilized with RNAlater (Qiagen, Germantown, MD, USA), snap frozen, and stored at -80°C
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tissue (~50 mg) was homogenized in 1 mL TRIzol Reagent (ThermoFisher Scientific, Waltham, MA, USA) following manufacturer’s protocol steps 1-8. After step 8, 0.4 mL of 200 proof ethanol was added and the samples briefly vortexed. The samples were loaded into RNeasy Mini Kit columns (cat. No. 74104, Qiagen, Germantown, MD, USA) and the manufacturer’s protocol followed from Part 1 step 3. Genomic DNA was removed with the RNase-free DNase Set (cat. No. 79254, Qiagen, Germantown, MD, USA) following manufacturer’s protocol.
Libraries were constructed and sequenced using the TruSeq LT Stranded RNA Sample Preparation Kit (Illumina, Inc., San Diego, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
AGA from litter 8 brought in with other litters in cohort 2
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| Data processing |
The libraries were pooled in equimolar concentration and the pool was quantitated by qPCR and sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1.
Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).
Each sample's fastq file run through trimmomatic 0.33 with the following parameters: ILLUMINACLIP:TruSeq3-SE.fa:2:15:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:15 MINLEN:30
NCBI's Sus scrofa 10.2 reference genome and annotation release 105 were indexed using STAR 2.5.2a with parameters --sjdbOverhang 99. Each sample was then aligned to the genome again using STAR 2.5.2a.
Read counts for each gene were generated using featureCounts (from subread v 1.5.0) with parameters -s 2 -g gene_id -t exon, where gene_id were Entrez Gene IDs that were manually pulled from the Dbxref attribute in the gene annotation release 105 gff file
Genome_build: Sus scrofa 10.2
Supplementary_files_format_and_content: tab-delimited text files of raw read counts per gene per sample were used directly in edgeR 3.16.5 for statistical analysis and thus are the "normalized" data.
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| Submission date |
Jul 23, 2019 |
| Last update date |
Feb 06, 2020 |
| Contact name |
Rodney W. Johnson |
| E-mail(s) |
rwjohn@uiuc.edu, godbout.2@osu.edu, jingchn@uiuc.edu
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| Phone |
217-333-2118
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| Fax |
217-333-8286
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| Organization name |
Univ of Illinois in Urbana
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| Department |
Animal Sciences
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| Lab |
Dr. Rodney Johnson's lab
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| Street address |
1207 W. Gregory Dr.
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| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
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| Platform ID |
GPL22475 |
| Series (1) |
| GSE134739 |
Hydrolyzed Fat Formula Increases Brain White Matter in Small for Gestational Age and Appropriate for Gestational Age Neonatal Piglets |
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| Relations |
| BioSample |
SAMN12344386 |
| SRA |
SRX6492421 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3965413_A8D14R2P_ACTTGAAT_L003_R1_001.qualtrim_Aligned.sortedByCoord.out_featCounts.txt.gz |
2.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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