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Sample GSM1955985 Query DataSets for GSM1955985
Status Public on Jan 19, 2017
Title I2_plate5_H_9
Sample type SRA
 
Source name Lin-CD34+CD38- bone marrow
Organism Homo sapiens
Characteristics fsc-a: 103322
fsc-w: 61396
fsc-h: 110289
ssc-a: 51033
ssc-w: 67597
ssc-h: 49477
lin: -80
cd34: 4023
cd10: 552
cd7: -38
cd45ra: 78
cd90: 3987
cd49f: 416
cd135: 1036
cd38: 847
facs time: 20437
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
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.
 
Submission date Nov 30, 2015
Last update date May 15, 2019
Contact name Lars Velten
E-mail(s) lars.velten@crg.eu
Organization name CRG
Department Bioinformatics and Genomics
Lab Velten lab
Street address C. Dr. Aiguader 88, P05
City Barcelona
ZIP/Postal code 08003
Country Spain
 
Platform ID GPL11154
Series (1)
GSE75478 Single-cell indexed RNA-Seq of human hematopoietic stem and progenitors
Relations
BioSample SAMN04300002
SRA SRX1454193

Supplementary file Size Download File type/resource
GSM1955985_counts_plate5_H_9.csv.gz 68.7 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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