|
| Status |
Public on Jul 21, 2016 |
| Title |
single HFF [HFF_Batch1.031] |
| Sample type |
SRA |
| |
|
| Source name |
human foreskin fibroblast
|
| Organism |
Homo sapiens |
| Characteristics |
passage: passage 8-12
facs sorting: not sorted
|
| Treatment protocol |
Growth can treatment conditions were listed in additional columns in the SAMPLE section
|
| Growth protocol |
Growth can treatment conditions were listed in additional columns in the SAMPLE section
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell suspentions were loaded onto a medium size (10-17 μm) C1 Single-Cell Auto Prep IFC (Fluidigm), and cell-loading script was performed according to the manufacturer’s instructions. Full-length single-cell cDNA libraries generated by the SMARTer PCR cDNA Synthesis kit (Clontech) and the Advantage 2 PCR kit (Clontech) performed in the C1 system.
For scRNA-seq, diluted single-cell cDNA libraries were fragmented and amplified using the Nextera XT DNA Sample Preparation Kit and the Nextera XT DNA Sample Preparation Index Kit (Illumina). Libraries were multiplexed at 24 libraries per lane, and single-end reads of 67-bp sequencing was performed on an Illumina HiSeq 2500 system. For bulk RNAseq, mRNA is isolated from purified 100 ng total RNA using oligo-dT beads. Isolated mRNA is fragmented in reverse transcription buffer with heat and then reverse-transcribed with SmartScribe reverse transcriptase using a random hexamer oligo.After reverse transcription, RNA is removed by RNaseA and RNaseH treatment. A partial Illumina 5′ adaptor is then ligated to the single stranded cDNA using T4 RNA ligase 1 and incubated overnight at 22°C. After purification, ligated cDNA is amplified by 18 cycles of PCR using oligos that contain full Illumina adaptors. Indexed cDNA libraries are pooled and sequenced on an Illumina HiSeq2500 with a single 51 bp read and a 10 bp index read.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Human foreskin fibroblast is cultured in DMEM/F12 with 10% FBS
sc_cell_type_ec.csv
HFF_Batch1.031
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Sequencing reads were mapped to hg19 using bowtie 0.12.8
Gene expected counts were calculated using RSEM 1.2.3
Genome_build: hg19
Supplementary_files_format_and_content: Expected counts
|
| |
|
| Submission date |
Dec 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ning Leng |
| E-mail(s) |
lengning1@gmail.com
|
| Organization name |
Morgridge Institute for Research
|
| Street address |
330 N Orchard St
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53715 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE75748 |
Snapshot and temporal scRNA-seq of progenitor cells to dissect human embryonic stem cells entry into endoderm progenitors |
|
| Relations |
| BioSample |
SAMN04321557 |
| SRA |
SRX1467678 |
