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Status |
Public on Jan 19, 2017 |
Title |
I2_plate4_B_12 |
Sample type |
SRA |
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Source name |
Lin-CD34+CD38- bone marrow
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Organism |
Homo sapiens |
Characteristics |
fsc-a: 82569 fsc-w: 68084 fsc-h: 79479 ssc-a: 72471 ssc-w: 67354 ssc-h: 70515 lin: 1013 cd34: 5929 cd10: 894 cd7: 58 cd45ra: 58 cd90: 4754 cd49f: 716 cd135: 2778 cd38: 136 facs time: 4999
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Extracted molecule |
polyA RNA |
Extraction protocol |
Fresh bone marrow mononuclear cells were stained with fluorescence labeled antibodies against CD34, CD38, CD45RA, CD90, CD49f, CD135, CD10, CD7 and a lineage cocktail consisting of CD4, CD8, CD11b, CD14, CD19, CD20, CD56 and CD235a. Single Lin-CD34+CD38- and LinCD34+CD38+ HSPCs were sorted into lysis buffer. Whole transcriptome amplifcation was performed using the QUARTZ-Seq protocol (Sasagawa et al., 2013). ERCC spike ins were included into the lysis buffer at a final dilution of 1:2,000,000. Libraries were constructed using Nextera Tn5 (Illumina) following the protocol provided, but using 1/4 of all volumes.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Data processing |
Demultiplexing. Perl 5.10.1 Trim off remaining poly-A tails, if applicable. Perl 5.10.1 Align reads to the human genome using GSNAP with default settings, expected paired-end length=400bp and allowable deviation from expected paired-end length=100bp. GSNAP version 2012-01-11 Count reads overlapping uniquely with mRNA genes. Python2.7/HTSeq Remove cells with less than 750 genes at a minimum of 10 reads per gene. R-3.1.2 Remove genes with less than 10 reads in at least 5 cells. R-3.1.2 Fit error models to the readcount data for normalization. R-3.1.2 / scde Remove cells with large overdispersion of the correlated component (theta_Corr < 0.45). R-3.1.2 Normalize data using posterior odds ratio, see manuscript. R-3.1.2 Genome_build: Homo Sapiens 37.68, with ERCC spike in sequences appended Supplementary_files_format_and_content: Comma separated text file. First column: ENSEMBL Gene id. Second column: Raw read count.
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Submission date |
Nov 30, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Lars Velten |
E-mail(s) |
lars.velten@crg.eu
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Organization name |
CRG
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Department |
Bioinformatics and Genomics
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Lab |
Velten lab
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Street address |
C. Dr. Aiguader 88, P05
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City |
Barcelona |
ZIP/Postal code |
08003 |
Country |
Spain |
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Platform ID |
GPL11154 |
Series (1) |
GSE75478 |
Single-cell indexed RNA-Seq of human hematopoietic stem and progenitors |
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Relations |
BioSample |
SAMN04300345 |
SRA |
SRX1454028 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1955820_counts_plate4_B_12.csv.gz |
67.3 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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