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Sample GSM4904702 Query DataSets for GSM4904702
Status Public on Sep 30, 2021
Title Plate number LC294
Sample type SRA
 
Source name Mouse retinal endothelial cells
Organism Mus musculus
Characteristics tissue: Retinal endothelial cells
strain: C57BL/6
age: P6
genotype: mixed sample (non-demultiplexed): Control;mTmG+ & Hbo1iEC/iEC;mTmG
Treatment protocol Mice were treated with 50 µg tamoxifen on P1 and P2 by intra-gastric injection to induce Cdh5-creERT2 mediated deletion of Hbo1 and drive expression of EGFP
Growth protocol Mice were intercrossed with the mTmG reporter allele that leads to cre-driven EGFP expression. Control mice were: Hbo1fl/+;Cdh5-creERT2+;mTmG+ and Hbo1iEC/iEC mice were: Hbo1flox/flox;Cdh5-creERT2+;mTmG.
Extracted molecule total RNA
Extraction protocol Retinas were removed at P6, dissociated into single cells using Liberase TM and Dnase I and stained for PECAM1. PECAM1+EGFP+ cells were flow sorted into a chilled 384-well PCR plate (Greiner, 785290) containing 1.2 μl of primer/lysis mix [20 nM indexed polydT primer (custom made, IDT), 1:6.000.000 dilution of ERCC RNA spike-in mix (Ambion, 4456740), 1 mM dNTPs (NEB, N0446S), 1.2 units SUPERaseIN Rnase Inhibitor (Thermo Fisher, AM2696), DEPC water (Thermo Fisher, AM9920)] using a BD FACSAria III flow cytometer (BD Biosciences, San Jose, CA, USA). Prepared RNA mixture plates were sealed and immediately frozen upside down at -80C.
Single cell transcriptome libraries were generated using the CelSeq2 protocol (Hashimshony et al., 2016 Genome Biol.) with the following adaptations: Second strand synthesis was performed using NEBNext Second Strand Synthesis module (NEB, #E6111S) in a final reaction volume of 8 µl and NucleoMag NGS Clean-up and Size select magnetic beads (Macherey-Nagel, 7449970.5) were used for all DNA purification and size selection steps.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing gene and ERCC count matrix generated using scPipe 1.10.0
reads were aligned using Rsubread 2.24.0
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: ERCC count matrix, rows represent ERCC spike-in sequences and each column is a well
Supplementary_files_format_and_content: gene count matrix, rows represent genes and each column is a well
Supplementary_files_format_and_content: sample sheet, rows represent a well and columns contain metadata on the sample in the well
 
Submission date Nov 11, 2020
Last update date Sep 30, 2021
Contact name Peter Hickey
E-mail(s) hickey@wehi.edu.au
Organization name WEHI
Street address 1G Royal Parade
City Parkville
ZIP/Postal code 3052
Country Australia
 
Platform ID GPL19057
Series (2)
GSE161310 The histone acetyltransferase HBO1 (KAT7) promotes efficient tip cell sprouting during angiogenesis
GSE161893 The histone acetyltransferase HBO1 (KAT7) promotes efficient tip cell sprouting during normal and pathogenic angiogenesis
Relations
BioSample SAMN16769049
SRA SRX9487850

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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