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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 19, 2016 |
| Title |
Adult_HSC_3722 |
| Sample type |
SRA |
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| Source name |
bonemarrow
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| Organism |
Mus musculus |
| Characteristics |
cell type: Haematopoietic stem cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T1 CD201-: CD31+CD45-CD41lowc-Kit+CD201low/-, T2 pre-HSCs: CD31+CD45+c-Kit+CD201high, T2 CD41low: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+; bonemarrow: Adult HSC: ESLAM(CD45+ EPCR+ CD48- CD150+).
FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
remove Illumina adaptor sequences, primer UP1, primer UP2 and 3’ ployA sequences using cutadapt (ver 1.6)
sequence alignment to the mouse genome (mm9) and spiked-in sequences using tophat (v2.0.12)
Cufflinks (v2.2.1) was used to estimate the expression level of each detected gene as fragment per kilobase of transcript per million fragments mapped (FPKM) value
Genome_build: mm9
Supplementary_files_format_and_content: fpkm_tracking (cufflinks output)
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| Submission date |
Sep 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xianlong Li |
| E-mail(s) |
acelixianlong@gmail.com
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| Organization name |
Peking University
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| Department |
Biodynamic Optical Imaging Center, College of Life Sciences
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| Street address |
5, Yiheyuan Rd., Haidian District
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE67120 |
Tracing the Formation of Haematopoietic Stem Cells in Mouse Embryos by Single-cell Functional and RNA-Seq Analyses [single-cell] |
| GSE67123 |
Tracing the formation of hematopoietic stem cells in mouse embryos by single-cell functional and RNA-Seq analyses |
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| Relations |
| BioSample |
SAMN04108605 |
| SRA |
SRX1283387 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1890044_Adult_HSC_3722.genes.fpkm_tracking.gz |
562.7 Kb |
(ftp)(http) |
FPKM_TRACKING |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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