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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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