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| Status |
Public on Aug 17, 2017 |
| Title |
2.5 dpc female HPG axis RNASeq of Kdm4a wildtype and knockout mice |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: We performed RNA-Seq on 2.5dpc mouse hypothalamus, pituitary, ovary and uterus of 8-10 week old littermate female control and Kdm4a knockout mice. Upon observing for the extent of altered genes of physiological relevance to observed female infertility phenotype, this would help us narrow down the most relevant tissue to perform genome wide ChipSeq binding profiles for Kdm4a, H3K4me3 and H3K9me3. This dataset would present likely target genes under direct control of Kdm4a.
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| Overall design |
Wildtype and Kdm4a knockout mice were set up for natural timed mating. At 2.5 dpc (days post coitus), females were sacrificed and checked for presence of preimplantation embryos by flushing the oviduct. Whole uterus, hypothalamus, pituitary and ovaries were dissected and immediately cleaned of fat and flash frozen in liquid nitrogen. RNA was extracted using Qiagen RNAeasyPlus mini kit following homogenization in RLTplus buffer., tissue RNA quality was measured using an Agilent 2100 Bioanalyzer system (Agilent, #G2940CA) and RNA 6000 Nano reagents (Agilent, #5067-1511). RIN scores were at least 8 for samples used in the RNA Seq with three biological replicates for each tissue
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| Contributor(s) |
Sankar A |
| Citation(s) |
28827393 |
| |
| Submission date |
Mar 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Aditya Sankar |
| E-mail(s) |
cnj376@ku.dk, aditya.sankar@embl.de
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| Organization name |
University of Copenhagen
|
| Department |
Biotech Research and Innovation Centre
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| Lab |
Helin
|
| Street address |
Ole Maaloes Vej 5
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (24)
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| This SubSeries is part of SuperSeries: |
| GSE96686 |
HTS-Seq analysis of Kdm4a wildtype and knockout females at 2.5 dpc |
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| Relations |
| BioProject |
PRJNA379376 |
| SRA |
SRP101992 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE96685_KO_Hypothalamus_counts.xlsx |
701.8 Kb |
(ftp)(http) |
XLSX |
| GSE96685_KO_Ovary_counts.xlsx |
700.9 Kb |
(ftp)(http) |
XLSX |
| GSE96685_KO_Pituitary_counts.xlsx |
688.9 Kb |
(ftp)(http) |
XLSX |
| GSE96685_KO_Uterus_counts.xlsx |
701.6 Kb |
(ftp)(http) |
XLSX |
| GSE96685_Kdm4a_2-5dpc_KO_vs_WT_Hypothalamus.xlsx |
1.8 Mb |
(ftp)(http) |
XLSX |
| GSE96685_Kdm4a_2-5dpc_KO_vs_WT_Ovary.xlsx |
2.0 Mb |
(ftp)(http) |
XLSX |
| GSE96685_Kdm4a_2-5dpc_KO_vs_WT_Pitutiary.xlsx |
1.8 Mb |
(ftp)(http) |
XLSX |
| GSE96685_Kdm4a_2-5dpc_KO_vs_WT_Uterus.xlsx |
1.9 Mb |
(ftp)(http) |
XLSX |
| GSE96685_WT_Hypothalamus_counts.xlsx |
724.0 Kb |
(ftp)(http) |
XLSX |
| GSE96685_WT_Ovary_counts.xlsx |
697.4 Kb |
(ftp)(http) |
XLSX |
| GSE96685_WT_Pituitary_counts.xlsx |
687.3 Kb |
(ftp)(http) |
XLSX |
| GSE96685_WT_Uterus_counts.xlsx |
699.2 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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