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Status |
Public on Mar 01, 2020 |
Title |
p0-cortex_WT_7 |
Sample type |
SRA |
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Source name |
cortex neuron
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 tissue: cortex neuron age: p0 genotype: wild type
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Extracted molecule |
polyA RNA |
Extraction protocol |
P0 mouse brain was dissected, and the tissue from cerebral cortex was digested with 0.013% of collagenase in Neurobasal Medium (Gibco) at 37℃ for 3 min. The collagenase was neutralized by adding excess amount of Neurobasal Medium. Single-cell suspension was made by gentle pipetting, and then filtered through 100-μm cell strainers.Single cells were then picked under the microscope by using a micro capillary pipette into the thin-walled PCR tube containing 2 µl of cell lysis buffer, 1 µl of oligo-dT primer and 1 µl of dNTP mix. First,reverse transcription is performed,the cDNA was pre-amplification by PCR. The cDNA library was then purified, tagmented, and ligated with adapters using the Nextera XT DNA Library Preparation kit (Illumina FC-131-1096).. Finally, the adapter-ligated fragments were further amplified by PCR and purified with AMPure XP beads (Beckman).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
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Description |
single-cell RNA-seq
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Data processing |
Single-cell RNA-seq reads were aligned to the mm38_tran genome assembly using hisat2 version 2.1.0 with parameters:-p 8 --mp 7,6 --sp 3,2 --rdg 6,5 --dta-cufflinks -x File format is transformed to BAM using samtools version 1.9 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks version 2.2.1 Genome_build: mm38_tran Supplementary_files_format_and_content: fpkm_tracking files include FPKM values for each Sample
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Submission date |
Aug 19, 2019 |
Last update date |
Mar 03, 2020 |
Contact name |
Xiao Ge |
Organization name |
Shanghai JiaoTong University
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Street address |
No. 800 Dongchuan Road
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City |
Shanghai |
ZIP/Postal code |
200240 |
Country |
China |
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Platform ID |
GPL21273 |
Series (2) |
GSE135394 |
Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [I] |
GSE138646 |
Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection |
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Relations |
BioSample |
SAMN12600583 |
SRA |
SRX6734558 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4038763_p0-cortex_WT_7.fpkm_tracking.gz |
741.5 Kb |
(ftp)(http) |
FPKM_TRACKING |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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