|
| Status |
Public on Feb 13, 2019 |
| Title |
Unfixed_SetA |
| Sample type |
SRA |
| |
|
| Source name |
Foreskin keratinocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Foreskin keratinocytes
condition: Unfixed cell
growth conditions: Keratinocyte Serum Free Medium
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Reverse Transcription from detergent and heat based lysates, according to the SORT-seq/CELseq2 protocol
CELseq2 library prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Read1 and Read2 where swapped to allow compatibility with CELseq2 pipeline
Reads were matched to individual cells using the demultiplexing function of the CELseq2 pipeline
Transcripts were Mapped and UMI corrected using standard settings of the CELseq2 pipeline - Reads were trimmed to 50 bases before mapping to UCSChg38 and hereafter matched to the gencode.v25.basic.annotation transcriptome
A count tables from all six samples was generated (UMI_Count_Table_JPGII170.tab.gz) where UnfixedA, UnfixedB, UnfixedC represent the unfixed cells and RAID-A, RAID-B, RAID-C represent the cells that were fixed and mock-stained according to the RAID procedure
For normalization, 40000 UMI counts were subsampled from all cells and cells with fewer counts were discarded. JPGII170_40K_SUB_GEO.csv.gz is the count table with the sampled counts
Genome_build: UCSChg38
Supplementary_files_format_and_content: The .csv.gz file contains 40000 sampled transcipt UMI counts for the cells from all 6 samples - samples are indicated in cell name
Supplementary_files_format_and_content: The tab.gz file contains contains raw transcipt UMI counts, as obtained from the CELseq2 pipeline, for the cells from all 6 samples - samples are indicated in cell name
|
| |
|
| Submission date |
Jun 15, 2018 |
| Last update date |
Feb 13, 2019 |
| Contact name |
Jan Patrick Gerlach |
| E-mail(s) |
janpgerlach@gmail.com
|
| Organization name |
Radboud Institute for Molecular Life Sciences
|
| Department |
Molecular Developmental Biology
|
| Street address |
Geert Grooteplein Zuid 28
|
| City |
Nijmegen |
| ZIP/Postal code |
6500HB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE115861 |
Comparison of single-cell transcriptomics quality between unfixed cells and cells that were fixed and mock stained according to the RAID procedure |
| GSE115981 |
RAID allows multiplexed quantification of intracellular (phospho-)proteins and transcriptomes from fixed single cells |
|
| Relations |
| BioSample |
SAMN09429722 |
| SRA |
SRX4221217 |
