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Sample GSM2689241 Query DataSets for GSM2689241
Status Public on Nov 11, 2017
Title P6_F3_LMPP
Sample type SRA
 
Source name cord blood
Organism Homo sapiens
Characteristics cell type: Cord blood CD34+ haemopoietic stem and progenitor cells
cell populations: LMPP
immunophenotype: Lin-CD34+CD38-CD90-/loCD45RA+CD10-
Treatment protocol Fresh Cord Blood cells were obtained and processed with ficoll to obtain mononuclear cells. CD34+ cells were purified using CD34 Microbead Kit and MACS separation columns
Growth protocol Fresh cord blood from normal donors were obtained with informed consent. They were processed within 16-34h after collection. Mononuclear cells were isolated and CD34+ fraction was separated as described{Quek et al, Journal of Experimental Medicine 2016}.
Extracted molecule polyA RNA
Extraction protocol Single cells were deposited in individual wells of 96 well plates, directly lysed according to the SmartSeq2 protocol and stored at -80C. No extraction protocol was performed
Single cell libraries for RNAseq were prepared using SmartSeq2 protocol (Picelli et al., Nature Protocols 2014) and the Illumina Nextera XT Index Kit (96 indexes, 384 samples, FC-131-1002) for cDNA tagmentation and indexing. ERCC RNA Spike-In Mix (Ambion, 4456740) are included.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing RNA-seq reads were aligned to hg19 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: hg19
Supplementary_files_format_and_content: HT-Seq counts (.txt)
 
Submission date Jun 28, 2017
Last update date May 15, 2019
Contact name Evangelia Diamanti
E-mail(s) ed347@cam.ac.uk
Phone 01223 62317
Organization name University of Cambridge
Department Haematology
Lab Gottgens
Street address Wellcome Trust / MRC Building, Hills Road
City Cambridge
ZIP/Postal code CB2 0XY
Country United Kingdom
 
Platform ID GPL20301
Series (1)
GSE100618 Single Cell RNA sequencing analysis of human haemopoietic lympho-myeloid progenitor populations (LMPP, MLP and GMP)
Relations
BioSample SAMN07290114
SRA SRX2965532

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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