|
| Status |
Public on Jan 01, 2020 |
| Title |
H1299_DMSO |
| Sample type |
SRA |
| |
|
| Source name |
H1299
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H1299
cell type: Non-small cell lung cancer
passage: 5 - 10
treatment: DMSO
|
| Treatment protocol |
Cells were treated with 500-nM DAC + 500-nM SB939 for a total of 72 and 18 h, respectively. Compound-containing media was refreshed every 24 h.
|
| Growth protocol |
H1299 cells were cultured in RPMI 1640 and HCT116 cells were grown in heat-inactivated McCoy’s 5A medium, both supplemented with 10% Fetal Bovine Serum, 0.4% Penicillin-Streptomycin and 1% L-glutamine.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
10x Genomics 5' single-cell RNA-seq
Please note that the first 26 positions of R1 contain the barcode (1:16) and UMI (17:26) sequences, followed by a constant part and biological sequence. R2 is purely biological and the I file contains the indices.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
CASAVA
Read pairs missing the constant part of the template switch oligo (defined by a hamming distance to TTTCTTATATGGG greater than 4) were excluded.
Filtered reads were processed with the cell-ranger analysis software version 2.1.0 and aligned against the human GRCh38-1.2.0 reference with the following parameters: chemistry = SC5P-PE; r1_length = 100; r2_length = 50; and outFilterMultimapScoreRange: 2 (STAR aligner specific)
Genome_build: hg38
Supplementary_files_format_and_content: Summarized molecule counts in a unique molecular identifier (UMI) matrix U = [Ufi] on features f and cells i
|
| |
|
| Submission date |
Oct 16, 2018 |
| Last update date |
Jan 01, 2020 |
| Contact name |
David Brocks |
| Organization name |
Weizmann Institute of Science
|
| Street address |
Herzlstreet 234
|
| City |
Rehovot |
| State/province |
Bavaria |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE121309 |
Single cell analysis reveals dynamics of transposable element expression following epigenetic de-repression |
|
| Relations |
| BioSample |
SAMN10246464 |
| SRA |
SRX4892657 |
