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| Status |
Public on Sep 14, 2018 |
| Title |
P0_CTX_cKO_NU08 |
| Sample type |
SRA |
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| Source name |
Cortex
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| Organism |
Mus musculus |
| Characteristics |
age: postnatal day 0
genotype: conditional knock-out
hemisphere: right
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Brain regions were dissected out and immediately flash frozen in liquid nitrogen. Total RNA was then purified from these samples, using an mRNeasy kit (Qiagen), following the manufacturer's instructions.
For P0 samples, Library construction was performed as a service by BGI America (Cambridge, MA). For P7 samples, mRNA was purified via poly(A) selection from 2ug of total RNA. Purified mRNA was then utilized to generated cDNA libraries using previously published protocols (Takahashi et al., 2015).
Pooled libraries of P0 and P7 brains were separately sequenced as 50 bp single-end on BGISEQ-500, a BGI in-house sequencer at BGI or as 75 bp single-end on Illumina NextSeq 500 at UT Southwestern Medical Center respectively.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Data processing |
Single-end reads (quality checked, filtered and adapter trimmed) were aligned to reference sequences (mm10 from UCSC) using STAR allowing three mismatches.
RNA-seq counts were quantified using HTSeq python suite. Reference gene model (mm10 GTF from Gencode vM11) were provided to assist the counting.
RNA-seq CPM values were then quantified using EdgeR (R package).
Gene-level CPM quantifications were used for all downstream processing.
Genome_build: UCSC Mouse GRCm38 / mm10
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| Submission date |
May 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Genevieve Konopka |
| E-mail(s) |
gena@alum.mit.edu
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| Organization name |
UT Southwestern Medical Center
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| Department |
Neuroscience
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| Street address |
5323 Harry Hines Blvd.
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| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-9111 |
| Country |
USA |
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| Platform ID |
GPL23479 |
| Series (1) |
| GSE98913 |
Cortical gene expression profiles in the forebrain-specific Foxp1 conditional knockout (cKO) mice at P0 and P7. |
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| Relations |
| BioSample |
SAMN07121202 |
| SRA |
SRX2822846 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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