|
| Status |
Public on Aug 21, 2019 |
| Title |
HEPS_AND1_MLLAF4_Sample3_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Human embryonic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Hemato-endothelial precursors
treatment: MLLAF4
day: Day15
|
| Extracted molecule |
total RNA |
| Extraction protocol |
HEPs were FACS-purified from day 15 EBs of EV or MA4-A4M expressing cells into individual wells of a 96-well PCR plate containing lysis buffer (0.2% Triton-X100 and 2.3 U of SUPERase-In RNase Inhibitor; Ambion).
Three independent replicates (50 cells/replicate) per condition were analyzed.
RNA/cDNA was obtained and amplified as per the SMARTSEQ2 protocol.
Single-cell RNA-seq analysis was performed as described previously (Picelli et al., 2014).
Pooled libraries were sequenced on the Illumina HiSeq 4000 platform.
Libraries were prepared for sequencing using the Illumina Nextera XT DNA preparation kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Single cell RNA-seq
processed data file: HTSeq_counts.txt
|
| Data processing |
RNA-seq reads were aligned to hg19 using STAR (version 2.4.2a) with parameters (--outFilterMultimapScoreRange 1 --outSAMstrandField intronMotif --genomeLoad NoSharedMemory).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: HTSeq_counts.txt: HT-Seq counts / gene counts.
|
| |
|
| Submission date |
Aug 22, 2018 |
| Last update date |
Aug 21, 2019 |
| Contact name |
Xiaonan Wang |
| Organization name |
Shanghai Jiao Tong University School of Medicine
|
| Department |
School of Public Health
|
| Street address |
227 Chongqing South Road
|
| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE118947 |
Enhanced hemato-endothelial specification during human embryonic development through developmental cooperation between AF4-MLL and MLL-AF4 fusions |
|
| Relations |
| BioSample |
SAMN09882771 |
| SRA |
SRX4597669 |
