Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

50:50 mixture of differentiated THP-1 macrophages and K562 cells treated with 1μg/ml of LPS, profiled with ChronoSeq for 12 samples barcoded with unique Time-Tags

ABSTRACT: The purpose of this experiment was to observe secondary signaling response of THP-1 to K562 cells observed in real time with ChronoSeq. Cells were sampled every 15 minutes. LPS was added 5 minutes after the first sample. Watchmaker RNAase inhibitor of 800U/μl was added to all Time-Tagged beads for a final concentration of 3U/μl, because of high RNAase activity in THP-1 supernatants.

INSTRUMENT(S): Illumina NovaSeq X

ORGANISM(S): Homo sapiens

SUBMITTER: Kanishk Asthana

PROVIDER: E-MTAB-15928 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

50:50 mixture of U937 and K562 cells treated with 0.5μg/ml of LPS, profiled with ChronoSeq for 12 samples barcoded with unique Time-Tags

Project description:The intent of the experiment was to observe the response of K562 cells when stimulated with LPS. To show that K562 cells cannot respond to LPS either alone or when mixed with cells unresponsive to LPS; we LPS stimulated a 50:50 mixture of K562 and undifferentiated U937 cells which are known to show limited or no response to LPS. Cells were stimulated with 0.5ug/ml of LPS with a sampling interval of 10 minutes.

2025-11-01 | E-MTAB-15927 | biostudies-arrayexpress

50:50 K562:EL4 (QC) at 430 cells/ μl with 10ng/ml TNF-α add 5 minutes after first sample and a sampling interval of 10 minutes. A total of three samples taken with ChronoSeq and tagged with three unique time-tags

Project description:This was a QC experiment to estimate the doublet rate with a species mixing experiment (Human+Mouse) at this cell concentration when used with the ChronoSeq device.

2025-11-01 | E-MTAB-15956 | biostudies-arrayexpress

50:50 K562:EL4 (QC) at 215 cells/ μl with 10ng/ml TNF-α add 5 minutes after first sample and a sampling interval of 10 minutes. A total of three samples taken with ChronoSeq and tagged with three unique time-tags

Project description:This was a QC experiment to estimate the doublet rate with a species mixing experiment at this cell concentration when used with the ChronoSeq device.

2025-11-01 | E-MTAB-15955 | biostudies-arrayexpress

Bulk K562 cells negative control (QC) for ChronoSeq with no stimulation, all 12 Time-Tags

Project description:Time-Tags were mixed 1 through 12. Data was also used for comparison with 10X Genomics 3' Chromium on K562 cells and with Single-Cell RNA-Seq negative control. Cells were not stimulated but maintained inside the ChronoSeq device for sampling. Samples were taken every 10 minutes.

2025-11-03 | E-MTAB-15966 | biostudies-arrayexpress

K562 Single-cell negative control with no stimulation. 12 samples were taken with ChronoSeq and barcodes with unique time-tags. Time-Tags injected from 12->1

Project description:Time-Tags were injected in reverse order to help detect any time-tag specific biases. Data was also used for comparison with 10X Genomics 3' Chromium on K562 cells

2025-11-01 | E-MTAB-15946 | biostudies-arrayexpress

K562 stimulated with TNFα with translation blocking using Puromycin. 12 samples were taken with ChronoSeq and barcodes with unique time-tags

Project description:We applied ChronoSeq to profile inflammatory responses in K562 cells stimulated with TNF-α, to capture the rapid NF-κB signaling cascade. 10 minute interval between samples including a 1 minute sampling duration. In addition Puromycin was added at a does of 5μg/ml for blocking translation. The purpose of this experiment was to measure TNF-α stimulation transcriptional program without translational feedback.

2025-11-01 | E-MTAB-15947 | biostudies-arrayexpress

K562+EL4 (Time Tag 10), K562(Time Tag 11), EL4 (Time Tag 12) (QC) 215 cells/ μl 3 Time-Tags. ChronoSeq No Stimulus. Only Checking Time-Tags with a Sampling Interval of 7minutes

Project description:Automated sampling within the ChronoSeq device showed similarly precise tagging: when human, mouse, and mixed reservoirs were processed in sequence, each cell population was exclusively labeled with its designated barcode. Goal of this experiment was to show accurate Time-Tagging of each sample with the ChronoSeq device.

2025-11-03 | E-MTAB-15964 | biostudies-arrayexpress

Bulk K562 and EL4 cells mixed with 12 Time-Tags for verification (QC) for ChronoSeq Beads

Project description:We checked our ability to uniquely identify each Time-Tag. We did this by mixing beads from odd numbered Time-Tags with human cells and even numbered Time-Tags with mouse cells manually in bulk. These beads were then washed and combined for Reverse Transcription, library preparation and sequencing. Time-Tag resolved cleanly into either human or mouse dominant with 1.6% or less mixed beads detected for each Time-Tag.

2025-11-03 | E-MTAB-15965 | biostudies-arrayexpress

K562 cells treated with 10ng/ml TNFα, profiled with ChronoSeq for 12 samples barcoded with unique Time-Tags

Project description:Both Live-cell imaging studies and scRNA-seq studies have shown multiple heterogeneous responses to the same stimulus in the same cells. Therefore as a first application we investigated if ChronoSeq could also reveal the heterogeneity in stimulus response; we applied ChronoSeq to profile inflammatory responses in K562 cells stimulated with TNF-α, to capture the rapid NF-κB signaling cascade. 10 minute interval between samples including a 1 minute sampling duration.

2025-11-01 | E-MTAB-15894 | biostudies-arrayexpress

proximity labeling 4T1 Cells through PCN

Project description:The 4T1 cells were labeled with BxxP via HA-PCN nanozyme as described above. After washing 5 times with PBS, cells were collected and lysed in RIPA buffer containing 1 % (v/v) Protease inhibitor cocktail (ThermoFisher Scientific) and 1 % (v/v) PMSF under bath-sonication, followed by centrifugation for 10 minutes at 4 ℃ to remove cell debris. Before the enrichment experiment, Pierce streptavidin magnetic beads (ThermoFisher Scientific) were washed twice with RIPA buffer for 2 minutes. The 400 μg samples were mixed with 50 μL beads slurry with rotation for 2 hours at 4 ℃, followed by washing twice with 1 mL RIPA buffer for 2 minutes, once with 1 mL 1 M KCl for 2 minutes, once with 1 mL 0.1 M Na(2)CO(3) for 2 minutes, once with 1 mL 2 M urea (pH=7.5) for 2 minutes, twice with RIPA buffer for 2 minutes []. Before enrichment, 100 μL cell lysis was packed as the input sample. For the western blotting analysis, the labeled proteins were eluted from the beads by boiling with protein loading buffer containing 20 mM dithiothreitol (DTT, ThermoFisher Scientific) and 2 mM biotin.

2025-07-29 | PXD057009 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data