|
| Status |
Public on Sep 14, 2018 |
| Title |
CD49f+ HSC [49f_subset_058] |
| Sample type |
SRA |
| |
|
| Source name |
cord blood derived CD49f+ haematopoietic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: human cord blood
passages: fresh
cell type: single cell CD49f+ HSC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD49f+ HSCs were purified by FACS from CD34+ cord blood samples obtained as in Notta et al., Science 2011. Novel subsets were defined as follows: CD49f+ Subset1 (CD19- CD38- CD45RA- CD90+ CD49f+ CD34lo CLEC9Ahi); CD49f+ Subset2 cells (CD19- CD38- CD45RA- CD90+ CD49f+ CD34hi CLEC9Alo), HSC/MPP Subset1 (CD19- CD38- CD45RA- CD34lo CLEC9Ahi) and HSC/MPP Subset2 (CD19- CD38- CD45RA- CD34hi CLEC9Alo). Single cell or pools of 20 cells were directly sorted into lysis buffer according to the Smart-seq2 protocol published by Picelli et al., Nat. Protocol 2014.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
SLX.12567.i721_i515
|
| 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: HTSeq counts (.txt)
|
| |
|
| Submission date |
Oct 16, 2017 |
| Last update date |
Sep 16, 2022 |
| Contact name |
Elisa Laurenti |
| Organization name |
University of Cambridge
|
| Department |
Haematology
|
| Lab |
Laurenti laboratory
|
| Street address |
Jeffrey Cheah Biomedical Centre
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0AW |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE104995 |
Single cell transcriptomes of cord blood derived subsets of human haematopoietic stem cells, LMPP and MLP myelo-lymphoid restricted progenitors [49f+ HSCs, 49f+ Subset1, 49f+ Subset2, Subset1, Subset2] |
| GSE115798 |
Single cell transcriptomes of cord blood derived subsets of human haematopoietic stem cells, LMPP and MLP myelo-lymphoid restricted progenitors |
|
| Relations |
| BioSample |
SAMN07787492 |
| SRA |
SRX3286615 |
