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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 28, 2020 |
| Title |
Squirrel Endometrium Individual 2 |
| Sample type |
SRA |
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| Source name |
Pregnant Squirrel
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| Organism |
Ictidomys tridecemlineatus |
| Characteristics |
tissue: endometrium
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the remaining tissue using the RNeasy Plus Mini Kit
Endometrial tissue samples from the pregnant uteri of baboon (x3), hamster (x3), bat (x2), and squirrel (x2) were dissected and mailed to the University of Chicago in RNA-Later. These samples were further dissected to remove myometrium, luminal epithelium, and extra-embryonic tissues, and then washed 3x in ice cold PBS to remove unattached cell debris and red blood cells. Total RNA was extracted from the remaining tissue using the RNeasy Plus Mini Kit (74134, QIAGEN) per manufacturer’s instructions. RNA concentrations were determined by Nanodrop 2000 (Thermo Scientific). A total amount of 2.5μg of total RNA per sample was submitted to the University of Chicago Genomics Facility for Illumina Next Gen RNA sequencing. Quality was assessed with the Bioanalyzer 2100 (Agilent). A total RNA library was generated using the TruSEQ stranded mRNA with RiboZero depletion (Illumina) for each sample. The samples were fitted with one of six different adapters with a different 6-base barcode for multiplexing. Completed libraries were run on an Illumina HiSEQ2500 with v4 chemistry on 2 replicate lanes for hamster and 1 lane for other species, of an 8 lane flow cell, generating 30-50 million 50bp single-end reads per sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Kallisto version 0.42.4 was used to pseudo-align the raw RNA-Seq reads to genomes
'kallisto index' with default parameters was used to build the genome index for each species
'kallisto quant' with the added parameters of 100 bootstraps, bias correction, and a flag for single end data with a !Sample_data_processing = fragment length of 50 and a standard deviation of 1 were used to quantify expression for each sample
Genome_build: Baboon (PapAnu2.0); Hamster (MesAur1.0); Bat (MyoLuc2.0); Squirrel (SpeTri2.0); Mouse (GRCm38)
Supplementary_files_format_and_content: Kallisto gene counts
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| Submission date |
Jul 27, 2020 |
| Last update date |
Feb 22, 2021 |
| Contact name |
Katelyn Mika |
| E-mail(s) |
kmmika12@gmail.com, kmmika@uchicago.edu
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| Organization name |
University of Chicago
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| Department |
Organismal Biology; Genetic Medicine
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| Lab |
Shubin, Basu
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| Street address |
1025 E. 57th Street
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platform ID |
GPL22929 |
| Series (1) |
| GSE155170 |
Evolutionary transcriptomics implicates HAND2 in the origins of implantation and regulation of gestation length |
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| Relations |
| BioSample |
SAMN15650417 |
| SRA |
SRX8830914 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4696527_Squirrel_Endometrium_Individual_2.txt.gz |
295.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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