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| Status |
Public on Dec 15, 2020 |
| Title |
ELA_rep2 |
| Sample type |
SRA |
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| Source name |
dorsal hippocampus
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: dorsal hippocampus
strain: Sprague-Dawley
age: 8 weeks
Sex: male
condition: Early-life adversity
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using the Qiagen RNeasy Kit, according to the manufacturer’s instructions.
Libraries were constructed using the Illumina TruSeq v2 kit with minor modifications. Briefly, 1 µg of total RNA was used as input, and poly(A) selection was carried out according to the protocol. Modifications to the TruSeq v2 protocol included a fragmentation time of 3 minutes. Additionally, 8 cycles of PCR were run for the enrichment of DNA fragments. Adapters were chosen according to protocol recommendations. Quantification of the libraries was accomplished using the KAPA qPCR kit for Illumina libraries.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
S2
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| Data processing |
RNA-seq read alignment (STAR, 2.5.0)
gene-level read counting (HTSeq, 0.6.1)
Genome_build: rn6
Supplementary_files_format_and_content: counts, tab-delimited
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| Submission date |
Nov 15, 2020 |
| Last update date |
Dec 15, 2020 |
| Contact name |
Anton Schulmann |
| E-mail(s) |
anton.schulmann@nih.gov
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| Organization name |
NIH/NIMH
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| Lab |
McMahon
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| Street address |
35 Convent Dr
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| City |
Bethesda |
| State/province |
Maryland (MD) |
| ZIP/Postal code |
20814 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE161498 |
Transcriptional effect of early-life adversity in adult hippocampus |
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| Relations |
| BioSample |
SAMN16803199 |
| SRA |
SRX9510399 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4908790_ELA_S2_count.txt.gz |
124.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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