|
Status |
Public on Nov 11, 2017 |
Title |
P5_G9_GMP |
Sample type |
SRA |
|
|
Source name |
cord blood
|
Organism |
Homo sapiens |
Characteristics |
cell type: Cord blood CD34+ haemopoietic stem and progenitor cells cell populations: GMP immunophenotype: Lin-CD34+CD38+CD123+CD45RA+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 |
SAMN07290079 |
SRA |
SRX2965378 |