|
| Status |
Public on Sep 14, 2018 |
| Title |
CD49f+ HSC Subset2 SLX.15683.i709_i517 |
| 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 Subset2
|
| Treatment protocol |
none
|
| Growth protocol |
none
|
| 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 HSC subsets were defined as follows: CD49f+ Subset2 cells (CD19- CD38- CD45RA- CD90+ CD49f+ CD34hi CLEC9Alo), HSC/MPP Subset2 (CD19- CD38- CD45RA- CD34hi CLEC9Alo). Myelo-lymphoid restricted progenitors were defined as follows: LMPP (CD19- CD38- CD34+ CD45RA+ CD10-), MLP (CD19- CD38- CD34+ CD45RA+ CD10+). Single 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.15683.i709_i517
|
| Data processing |
gsnap version 2015-09-29 was used to map reads onto the human reference genome GRCh38. Parameters used: -A sam -B 5 -t 24 -n 1 -Q -N 1. The result output would be in the format of sam files.
A python HTSeq (version 0.5.3p3) was used to generate read counts text files using the output of gsnap sam files as input.
Genome_build: GRCh38
Supplementary_files_format_and_content: HTSeq counts (.csv)
|
| |
|
| Submission date |
Jun 11, 2018 |
| 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) |
| GSE115639 |
Transcriptome of cord blood derived subsets of human haematopoietic stem cells, LMPP and MLP myelo-lymphoid restricted progenitors [49f+ Subset2, Subset2, LMPPs, MLPs] |
| GSE115798 |
Single cell transcriptomes of cord blood derived subsets of human haematopoietic stem cells, LMPP and MLP myelo-lymphoid restricted progenitors |
|
| Relations |
| BioSample |
SAMN09395598 |
| SRA |
SRX4194596 |
