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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 27, 2021 |
| Title |
microglia (Ad-PPAR-r treated animal) [3-K196-4] |
| Sample type |
SRA |
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| Source name |
microglia isolated by FACS
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| Organism |
Oryctolagus cuniculus |
| Characteristics |
breed: New Zealand
disease state: Intraventricular hemorrhage (IVH)
tissue: Brain
cell type: CD11-positive CD45-low microglia
treatment: Ad-PPARg
antibody: mouse anti-rabbit CD45, Bio-Rad, MCA808GA; Rat anti-CD11b-dylight550, Novus, NB600-1327R
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| Treatment protocol |
The rabbit kits with moderate-to-severe IVH were treated with intracerebroventricular (ICV) Ad-GFP or Ad-PPARg-GFP (CMV promoter, 5 µl volume) 1 mm ant., 4 mm lateral and 3 mm deep from Bregma under anesthesia. We compared Ad-GFP and Ad-PPARg-GFP treated kits.
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| Growth protocol |
NA
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction, library preparations, sequencing reactions and bioinformatic analysis were carried out by GENEWIZ, LLC (South Plainfield, NJ, USA). RNA samples were extracted using Trizol (Invitrogen, Carlsbad, CA). Extracted samples were quantified by Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was measured using the RNA Screen Tape on Agilent 2200 TapeStation (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared and validated using DNA Analysis Screen Tape on the Agilent 2200 TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by qPCR (KAPA Biosystems, Wilmington, MA, USA). The pooled libraries were clustered on a flowcell, which were loaded on the Illumina HiSeq instrument (4000) according to manufacturer’s instructions and sequenced using a 2x150 bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Hiseq Control software was used for basecalling.
Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Sequenced reads were trimmed for adaptor sequence, trimmed reads were mapped to the Rabbit Oryctolagus reference genome available on ENSEMBL using the STAR aligner version 2.5.2b.
Unique gene hit counts were calculated by using feature counts from Subread package version 1.5.2.
Gene counts were normalized to the median and the average expression level and coefficient of variation among biological replicas.
Genome_build: OryCun 2.0
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include raw counts.
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| Submission date |
Aug 24, 2021 |
| Last update date |
Aug 27, 2021 |
| Contact name |
Praveen Ballabh |
| E-mail(s) |
praveen.ballabh@einsteinmed.org
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| Phone |
718-430-3853
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| Organization name |
ALBERT EINSTEIN COLLEGE OF MEDICINE
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| Department |
Pediatrics and Neuroscience
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| Lab |
Ballabh lab
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| Street address |
1410 Pelham Parkway South
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| City |
BRONX |
| State/province |
New York |
| ZIP/Postal code |
10461 |
| Country |
USA |
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| Platform ID |
GPL25392 |
| Series (1) |
| GSE182718 |
PPARg activation enhances myelination and neurological recovery in premature rabbits with intraventricular hemorrhage |
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| Relations |
| BioSample |
SAMN20965985 |
| SRA |
SRX11899975 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5535610_3-K196-4-PPARr.counts.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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