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Sample GSM4301529 Query DataSets for GSM4301529
Status Public on Jan 16, 2023
Title um_berninger_2019_01_003_p1_C01_1c_S3
Sample type SRA
 
Source name adult neural stem cell
Organism Mus musculus
Characteristics cell type: adult neural stem cell
treatment: control virus
days post-treatment: 3
Growth protocol Mice were administrated with lentivirus which encode EGFP or Yap1 5SA. DG was dissected from hippocampus and the tissue was enzymatically dissociated in Neural Tissue Dissociation Kit (Miltenyi Biotec, Germany). Dissociation was stopped by adding 10 ml HBSS (Ca+, Mg+) (Invitrogen). Cells were filtered by 70 µm cell strainer, then centrifuged at 300 g for 10 min. Single cell suspension was resuspended with PBS which contains 5% FBS.
Extracted molecule polyA RNA
Extraction protocol All the EGFP positive cells were collected into lysis buffer of 96-wells plates directly by Aria II SORP cell sorter at single cell sorting mode.
Libraries were prepared using the Illumina Nextera XT DNA sample preparation kit. The protocol is based on the Tagmentation protocol from Fluidigm, which uses ¼ of the reagents per tagmentation reaction with a starting amount of 100-125pg of cDNA. Through this tagmentation step, the cDNA is fragmented and partial Nextera adaptors are added to each end of the cDNA fragments. A PCR follows, which adds the rest of the Nextera adaptors and the i5 and i7 dual indexes. Libraries were amplified in 12 PCR cycles. Three microliters of each library were pooled into a single tube and the pool was subsequently bead purified using Agencout AMPure XP beads, with a ratio of 0.9:1 Beads:DNA. The purified pool was profiled in a High Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). Four pools (coming from four 96-well plates) are again pooled together in equimolar ratio and sequenced in a single NextSeq 500 Highoutput Flowcell, single read for 1x 75 cycles for read 1 plus 2x 8 cycles for each index read.
scRNA-Seq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Control-d03
expression of control virus in adult neural stem cells for 3 days
Data processing Smart-Seq2 raw data demultiplexing was performed using Illumina’s bcl2fastq conversion software v.2.19.1 and overall sequence quality was assessed with FastQC v0.11.5. .
STAR v.2.5.2b with default parameters (except –outFilterMismatchNoverLmax 0.04) was used to align reads to the mouse reference genome GRCm38 (mm10), which was supplemented with ERCC RNA Spike-In Mix (ThermoFischer) control sequences and the GTF gene annotation from Ensembl release 88.
Read summarization at the gene level was performed using Subread featureCounts v.1.6.2 with default parameters.
Genome_build: GRCm38 with ERCC control sequences
Supplementary_files_format_and_content: Raw count matrix with genes in rows and cells in columns
 
Submission date Feb 07, 2020
Last update date Jan 16, 2023
Contact name Gregorio Alanis-Lobato
E-mail(s) g.alanis.lobato@gmail.com
Organization name Boehringer Ingelheim Pharma
Department Global Computational Biology and Digital Sciences
Street address Birkendorfer Str 65
City Biberach an der Riss
ZIP/Postal code 88400
Country Germany
 
Platform ID GPL13112
Series (1)
GSE144967 The transcriptional co-activator Yap1 promotes adult hippocampal neural stem cell activation
Relations
BioSample SAMN14066362
SRA SRX7693383

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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