|
Status |
Public on Jan 01, 2020 |
Title |
HCT116_DMSO |
Sample type |
SRA |
|
|
Source name |
HCT116
|
Organism |
Homo sapiens |
Characteristics |
cell line: HCT116 cell type: Colorectal 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.
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|
|
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
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|
|
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 |
SAMN10246461 |
SRA |
SRX4892659 |