title: day6_SM_139

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW19


title: day6_SM_138

status: Public on Jan 10 2023

type: SRA

city: Kyoto city

first: Ryosuke

last: Yamamoto

state: Kyoto pref

address: 54 Kawahara-cho

department: Department of Otolaryngology, Head and Neck Surgery

country: Japan

institute: Kyoto University

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW18

library_source: transcriptomic single cell

data_processing:
Demultiplexing: C1 mRNA Seq HT Demultiplex Script v2.0 (Fluidigm)
Mapping: STAR v2.7.0a
Gene counting: SUBREAD v1.6.3
Normalization: Transcripts per million (TPM), quantile normalization (quminorm v0.1.0), sctransform (sctransform v0.3.3)
Assembly: GRCg6a, GCF_000002315.6
Supplementary files format and content: raw_count_file.txt: Unfiltered, non-normalized count file
Supplementary files format and content: normalized_count_file.txt: Filtered, normalized count file (TPM, quantile normalization)
Supplementary files format and content: normalized_seurat_obj.rds: Filtered, normalized Surat object file  (TPM, quantile normalization, scTransform)

molecule: total RNA

organism: Gallus gallus

source_name: basilar papillae

extract_protocol:
BP specimens were incubated in prewarmed 500 µg/ml thermolysin in medium 199 at 37℃ for 30 min. To stop enzymatic dissociation, specimens were transferred into medium 199 supplemented with 5% FBS. Afterwards, the BP was separated from the surrounding tissues under the stereomicroscope. Then, the samples were transferred into an Eppendorf tube by a pipette. After centrifugation (800g x 5 min) at room temperature, the supernatant was removed. Samples were incubated in an enzyme cocktail containing 50% Accutase and 50% TrypLE Select enzyme for 7 min at 37℃. After gently pipetting 10-20 times, samples were incubated for additional 4 min at 37℃. After inactivation of enzymatic activity with medium 199 supplemented with 5% FBS, further mechanical dissociation by pipetting was performed. Dissociated cells were collected after centrifugation and resuspended in medium 199 supplemented with 5% FBS.
Capture of the single cells and cDNA synthesis were conducted using C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2 (Fluidigm), according to manufacturer’s instruction. Briefly, 12,000 cells of each sample were loaded onto HT IFC, and 400 cells were captured in the IFC. Sequencing libraries were prepared by transposase-assisted tagmentation and enrichment of 3’end of genes using Nextera XT DNA Library Prep Kit (Illumina). The libraries were sequenced on the HiSeq2500 for 25 and 75 cycles paired-end reads.

treatment_protocol: Basilar papillae (BPs) were dissected from the temporal bones (intact) and incubated in the control medium for 24 h (day0_pre). BPs were cultured with 78 microM stereptomycin for 48 h (day2_SM). A part of BPs were maintained additional 96 h in the control medium (day6_SM). Other BPs were cultured in the control medium for 48 h (day2_ctrl) or 144 h (day6_ctrl)

tag: tissue

value: basilar papillae

tag: treatment

value: 48-h exposure to SM + 96-h culture


title: day6_SM_141

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW21


title: day6_SM_140

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW20


title: day6_SM_135

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW15


title: day6_SM_136

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW16


title: day6_SM_137

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW17


title: day6_SM_134

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW14


title: day6_SM_156

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW36


title: day6_SM_152

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW32


title: day6_SM_130

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW10


title: day6_SM_132

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW12


title: day6_SM_131

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW11


title: day6_SM_126

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW06


title: day6_SM_128

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW08


title: day6_SM_125

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW05


title: day6_SM_129

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW09


title: day6_SM_123

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW03


title: day6_SM_127

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW07


title: day6_SM_121

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW01


title: day6_SM_120

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW40


title: day6_SM_119

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW39


title: day6_SM_124

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW04


title: day6_SM_122

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW02


title: day6_SM_117

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW37


title: day6_SM_116

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW36


title: day6_SM_115

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW35


title: day6_SM_118

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW38


title: day6_SM_133

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC470_ROW13


title: day6_SM_112

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW32


title: day6_SM_113

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW33


title: day6_SM_109

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW29


title: day6_SM_106

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW26


title: day6_SM_114

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW34


title: day6_SM_105

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW25


title: day6_SM_103

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW23


title: day6_SM_102

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW22


title: day6_SM_101

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW21


title: day6_SM_104

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW24


title: day6_SM_099

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW19


title: day6_SM_100

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW20


title: day6_SM_098

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW18


title: day6_SM_096

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW16


title: day6_SM_111

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW31


title: day6_SM_095

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW15


title: day6_SM_097

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW17


title: day6_SM_108

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW28


title: day6_SM_110

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW30


title: day6_SM_107

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW27


title: day6_SM_091

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW11


title: day6_SM_090

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW10


title: day6_SM_093

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW13


title: day6_SM_086

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW06


title: day6_SM_087

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW07


title: day6_SM_085

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW05


title: day6_SM_083

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW03


title: day6_SM_094

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW14


title: day6_SM_082

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW02


title: day6_SM_089

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW09


title: day6_SM_084

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW04


title: day6_SM_081

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW01


title: day6_SM_080

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW40


title: day6_SM_075

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW35


title: day6_SM_077

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW37


title: day6_SM_088

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW08


title: day6_SM_078

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW38


title: day6_SM_079

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW39


title: day6_SM_076

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW36


title: day6_SM_072

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW32


title: day6_SM_073

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW33


title: day6_SM_092

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC469_ROW12


title: day6_SM_071

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW31


title: day6_SM_069

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW29


title: day6_SM_066

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW26


title: day6_SM_065

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW25


title: day6_SM_067

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW27


title: day6_SM_064

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW24


title: day6_SM_068

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW28


title: day6_SM_070

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW30


title: day6_SM_058

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW18


title: day6_SM_057

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW17


title: day6_SM_055

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW15


title: day6_SM_059

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW19


title: day6_SM_060

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW20


title: day6_SM_056

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW16


title: day6_SM_062

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW22


title: day6_SM_054

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW14


title: day6_SM_074

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW34


title: day6_SM_052

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW12


title: day6_SM_050

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW10


title: day6_SM_046

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW06


title: day6_SM_045

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW05


title: day6_SM_044

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW04


title: day6_SM_051

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW11


title: day6_SM_047

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW07


title: day6_SM_043

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW03


title: day6_SM_048

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW08


title: day6_SM_041

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW01


title: day6_SM_063

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW23


title: day6_SM_040

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW40


title: day6_SM_038

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW38


title: day6_SM_036

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW36


title: day6_SM_035

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW35


title: day6_SM_039

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW39


title: day6_SM_034

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW34


title: day6_SM_028

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW28


title: day6_SM_033

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW33


title: day6_SM_049

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW09


title: day6_SM_027

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW27


title: day6_SM_031

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW31


title: day6_SM_026

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW26


title: day6_SM_029

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW29


title: day6_SM_023

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW23


title: day6_SM_024

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW24


title: day6_SM_061

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW21


title: day6_SM_042

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW02


title: day6_SM_022

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW22


title: day6_SM_020

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW20


title: day6_SM_021

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW21


title: day6_SM_037

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW37


title: day6_SM_018

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW18


title: day6_SM_025

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW25


title: day6_SM_019

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW19


title: day6_SM_032

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW32


title: day6_SM_013

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW13


title: day6_SM_016

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW16


title: day6_SM_017

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW17


title: day6_SM_015

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW15


title: day6_SM_012

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW12


title: day6_SM_011

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW11


title: day6_SM_010

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW10


title: day6_SM_030

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW30


title: day6_SM_007

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW07


title: day6_SM_014

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW14


title: day6_SM_004

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW04


title: day6_SM_006

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW06


title: day6_SM_053

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC468_ROW13


title: day6_SM_005

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW05


title: day6_SM_003

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW03


title: day6_ctrl_400

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW40

value: 144-h culture


title: day6_SM_002

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW02


title: day6_SM_001

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW01


title: day6_ctrl_398

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW38


title: day6_ctrl_399

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW39


title: day6_ctrl_396

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW36


title: day6_ctrl_397

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW37


title: day6_ctrl_394

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW34


title: day6_ctrl_391

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW31


title: day6_ctrl_393

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW33


title: day6_ctrl_395

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW35


title: day6_ctrl_392

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW32


title: day6_ctrl_389

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW29


title: day6_ctrl_390

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW30


title: day6_SM_008

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW08


title: day6_ctrl_388

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW28


title: day6_ctrl_382

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW22


title: day6_ctrl_385

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW25


title: day6_ctrl_383

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW23


title: day6_ctrl_387

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW27


title: day6_ctrl_384

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW24


title: day6_ctrl_386

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW26


title: day6_ctrl_379

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW19


title: day6_ctrl_378

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW18


title: day6_ctrl_381

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW21


title: day6_ctrl_380

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW20


title: day6_ctrl_377

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW17


title: day6_ctrl_375

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW15


title: day6_ctrl_374

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW14


title: day6_ctrl_371

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW11


title: day6_SM_009

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC467_ROW09


title: day6_ctrl_370

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW10


title: day6_ctrl_373

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW13


title: day6_ctrl_372

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW12


title: day6_ctrl_369

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW09


title: day6_ctrl_366

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW06


title: day6_ctrl_365

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW05


title: day6_ctrl_367

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW07


title: day6_ctrl_364

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW04


title: day6_ctrl_363

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW03


title: day6_ctrl_362

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW02


title: day6_ctrl_361

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW01


title: day6_ctrl_358

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW38


title: day6_ctrl_359

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW39


title: day6_ctrl_357

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW37


title: day6_ctrl_353

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW33


title: day6_ctrl_360

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW40


title: day6_ctrl_354

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW34


title: day6_ctrl_356

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW36


title: day6_ctrl_376

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW16


title: day6_ctrl_352

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW32


title: day6_ctrl_349

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW29


title: day6_ctrl_348

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW28


title: day6_ctrl_351

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW31


title: day6_ctrl_347

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW27


title: day6_ctrl_345

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW25


title: day6_ctrl_346

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW26


title: day6_ctrl_344

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW24


title: day6_ctrl_368

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC466_ROW08


title: day6_ctrl_342

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW22


title: day6_ctrl_340

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW20


title: day6_ctrl_338

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW18


title: day6_ctrl_336

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW16


title: day6_ctrl_341

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW21


title: day6_ctrl_339

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW19


title: day6_ctrl_337

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW17


title: day6_ctrl_334

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW14


title: day6_ctrl_331

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW11


title: day6_ctrl_330

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW10


title: day6_ctrl_329

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW09


title: day6_ctrl_355

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW35


title: day6_ctrl_326

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW06


title: day6_ctrl_325

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW05


title: day6_ctrl_333

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW13


title: day6_ctrl_350

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW30


title: day6_ctrl_328

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW08


title: day6_ctrl_332

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW12


title: day6_ctrl_324

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW04


title: day6_ctrl_323

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW03


title: day6_ctrl_327

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW07


title: day6_ctrl_322

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW02


title: day6_ctrl_321

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW01


title: day6_ctrl_320

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW40


title: day6_ctrl_343

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW23


title: day6_ctrl_319

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW39


title: day6_ctrl_318

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW38


title: day6_ctrl_316

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW36


title: day6_ctrl_315

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW35


title: dph2-del, DTA induction, rep1

city: Bethesda

first: Byung-Sik

last: Shin

state: Maryland

address: 6 Center Dr, BLDG 6, RM 227

country: USA

institute: NIH

library_source: transcriptomic

data_processing:
Library strategy: Ribo-Seq
Sequencing data were provided by NHLBI DNA Sequencing and Genomics Core (NIH)
Linker was removed by cutadapt 2.8 with Python 3.7.5
After sorting the sequences by sample barcodes, PCR duplicates were removed by custom Python script.
rRNAs, tRNAs and other non-coding RNAs were removed by bowtie 1.1.2.
Alignments were done by bowtie 1.1.2 with the option -v 2 -m 1 -a -y --best --strata
Genome_build: Yeast trascriptome of R64-1-1 S288C reference genome assembly (SacCer3) was used. 3' and 5' UTR information was from Pelechano and Steinmetz (Nature 2013) and modified by Ingolia.

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Yeast cells were grown to A600 0.6-1.0 in selective media.

extract_protocol:
Yeast cells were lysed by grinding by Freezer Mill. CHO cells were lysed by lysis buffer containing Triton X-100. Ribosomes were collected by sucrose cushion with ultracentrifugation. RNAs were extract by Direct-zol RNA Microprep Kits.
Libraries were prepared according to published protocol by Ingolia (Methods 2017)
Ribosome protected fragments (riboseq)

treatment_protocol: Refer to SAMPLES treatment columns

tag: strain

value: Cultured cell

tag: genotype

value: eEF2-WT, dph2-del

value: DTA induction

tag: agent

value: cycloheximide + tigecycline


title: day6_ctrl_314

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW34


title: DPH2, DTA induction, rep2

value: eEF2-WT, DPH2


title: day6_ctrl_313

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW33


title: day6_ctrl_335

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC465_ROW15


title: day6_ctrl_312

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW32


title: DPH2, DTA induction, rep1


title: day6_ctrl_311

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW31


title: day6_ctrl_310

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW30


title: day6_ctrl_308

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW28


title: OL14, SK-MEL, rep3

city: Bar Harbor

first: Ryan

last: Tewhey

state: ME

address: 600 Main Street

institute: Jackson Laboratory

data_processing:
MPRAmatch, MPRAcount (https://github.com/tewhey-lab/MPRA_oligo_barcode_pipeline)
MPRAmodel (https://github.com/tewhey-lab/MPRAmodel)
Supplementary files format and content: Tab-separated file containing individual barcode counts for each replicate

organism: synthetic construct

extract_protocol: none provided by the submitter

tag: cell line


title: day6_ctrl_307

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW27


title: day6_ctrl_309

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW29


title: OL14, SK-MEL, rep4


title: OL14, SK-MEL, rep2


title: OL14, SK-MEL, rep5


title: OL14, SK-MEL, rep1


title: OL14, Plasmid, rep4

library_source: genomic

molecule: genomic DNA


title: OL14, Plasmid, rep3


title: day6_ctrl_306

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW26


title: day6_ctrl_317

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW37


title: OL14, Plasmid, rep5


title: day6_ctrl_304

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW24


title: dph2-del, DTA induction, rep2


title: day6_ctrl_305

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW25


title: day6_ctrl_303

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW23


title: OL14, Plasmid, rep2


title: day6_ctrl_302

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW22


title: OL14, Jurkat, rep6

source_name: Jurkat

value: Jurkat


title: OL14, Jurkat, rep4


title: day6_ctrl_299

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW19


title: day6_ctrl_301

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW21


title: OL14, Jurkat, rep3


title: day6_ctrl_298

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW18


title: day6_ctrl_297

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW17


title: day6_ctrl_296

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW16


title: OL14, HT29, rep5


title: OL14, HT29, rep4


title: day6_ctrl_294

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW14


title: day6_ctrl_295

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW15


title: OL14, Jurkat, rep1


title: OL14, HT29, rep3


title: day6_ctrl_292

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW12


title: OL14, HT29, rep1


title: OL14, HT29, rep2


title: OL14, deltaGFP, rep2


title: day6_ctrl_293

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW13


title: OL14, deltaGFP, rep1


title: day6_ctrl_289

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW09


title: OL14, Plasmid, rep1


title: day6_ctrl_291

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW11


title: OL14, Jurkat, rep5


title: day6_ctrl_290

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW10


title: day6_ctrl_288

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW08


title: day6_ctrl_287

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW07


title: MP-51, condition7-Rifampicine treated

city: Chicago

first: Minoli

last: Perera

state: Illinois

address: 303 E. Chicago Avenue, Ward 9-188

department: Pharmacology

institute: Northwestern University

data_processing:
RNA-QC was performed using an Agilent Bio-analyzer. RNA-SEQ libraries were generated using Illumina mRNA TruSeq kits and sequenced on an Illumina HiSEQ2500 or 4000 according to Illumina provided protocols.
Post alignment and QC, reads were mapped to genes referenced with comprehensive gene annotation (GENCODE version 25) by HTSeq (version 0.6.1p1) with union mode and minaqual = 20
HTSeq raw counts were supplied for gene expression analysis and were normalized using regularized log transformation and principal component analysis (PCA) using Bioconductor package DESeq2 (version1.20.0)
We calculated TPM (transcript per million) by first normalizing the counts by gene length and then normalizing by read depth (Wagner, Kin, & Lynch, 2012). Gene expression values were filtered based on the expression thresholds > 0.1 TPM in at least 20% of samples and ≥ 6 reads in at least 20% of samples as done in the GTEx consortium (gtexportal.org, Analysis Methods, V7).
We normalized expression values across samples by TMM (trimmed mean of M-values) implemented in edgeR (Robinson & Oshlack, 2010) and then normalized for each gene by inverse normal transformation.
Genome_build: hg37
Assembly: GRCh37.p13
Supplementary files format and content: Sample_MP-XX2count.txt data contain raw count data from Htseq for condition2- Omeprazole drug treatment
Supplementary files format and content: Sample_MP-XX3count.txt data contain raw count data from Htseq for condition3 - Phenobarbital drug treatment
Supplementary files format and content: Sample_MP-XX4count.txt data contain raw count data from Htseq for condition4 - Dexamethasone drug treatment
Supplementary files format and content: Sample_MP-XX5count.txt data contain raw count data from Htseq for condition5 - Carbamazepine drug treatment
Supplementary files format and content: Sample_MP-XX6count.txt data contain raw count data from Htseq for condition6 - Phenytoin drug treatment
Supplementary files format and content: Sample_MP-XX7count.txt data contain raw count data from Htseq for condition7 - Rifampicine  drug treatment
Supplementary files format and content: condition2_Omeprazole_expression_tmm_normalization_exp.txt contain TMM normalized expression values across samples for condition2 - Omeprazole drug treatment
Supplementary files format and content: condition3_Phenobarbital_expression_tmm_normalization_exp.txt contain TMM normalized expression values across samples for condition3 - Phenobarbital drug treatment
Supplementary files format and content: condition4_Dexamethasone_expression_tmm_normalization_exp.txt contain TMM normalized expression values across samples for condition4 - Dexamethasone drug treatment
Supplementary files format and content: condition5_Carbamazepine_expression_tmm_normalization_exp.txt contain TMM normalized expression values across samples for condition5 - Carbamazepine drug treatment
Supplementary files format and content: condition6_Phenytoin_expression_tmm_normalization_exp.txt contain TMM normalized expression values across samples for condition6 - Phenytoin drug treatment
Supplementary files format and content: condition7_Rifampicine_expression_tmm_normalization_exp.txt contain TMM normalized expression values across samples for condition7 - Rifampicine  drug treatment

organism: Homo sapiens

source_name: liver hepatocyte cells

growth_protocol: Cell were plated at a density of 0.6 x 106 cells/well in 500 µL InVitroGro-CP media (BioIVT, Baltimore, MD) in collagen-coated plates with matrigel (Corning, Bedford, MA) overlay and incubated overnight at 37° C. Cultures were maintained in InVitroGro-HI media (BioIVT) supplemented with Torpedo antibiotic mix (BioIVT) per the manufacturer's instructions. The media was replaced every 24 hours for three days.

extract_protocol: RNA was extracted after three days using the RNeasy Plus mini-kit (Qiagen) per manufacturer's instructions. RNA-QC was performed using an Agilent Bio-analyzer. RNA-SEQ libraries were generated using Illumina mRNA TruSeq kits.

treatment_protocol: Hepatocyte suspensions (0.6 x 10^6 cells in 0.5 mL of CP medium) were added to collagen-coated wells of a 24-well plate followed by incubation at 37° C for 4-5 hours to allow cells to adhere. The CP medium was replaced with 0.5 mL of 0.25 mg/mL matrigel solution in HI medium, and plates were incubated overnight at 37° C. The following day, matrigel-medium was replaced with 0.5 mL of induction drug in HI medium with antibiotics and the step was repeated for the next two consecutive days after every 24 hours. We performed the induction experiments using the following six drugs: Omeprazole (50 μM), Phenobarbital sodium (1 mM), Dexamethasone (50 μM), Carbamazepine (50 μM), Phenytoin (75 μM), Rifampicine (25 μM).

tag: gender

value: Male

tag: age

tag: platform

tag: batch

tag: cell type

value: liver hepatocyte cells

value: Rifampicine drug


title: day6_ctrl_300

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW20


title: day6_ctrl_286

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW06


title: MP-49, condition7-Rifampicine treated

description: condition7_Rifampicine_expression_tmm_normalization_exp.txt

value: Female


title: MP-45, condition7-Rifampicine treated


title: day6_ctrl_285

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW05


title: OL14, Jurkat, rep2


title: MP-52, condition7-Rifampicine treated


title: MP-44, condition7-Rifampicine treated


title: day6_ctrl_284

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW04


title: day6_ctrl_282

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW02


title: MP-43, condition7-Rifampicine treated


title: MP-42, condition7-Rifampicine treated


title: day6_ctrl_281

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW01


title: MP-39, condition7-Rifampicine treated


title: MP-40, condition7-Rifampicine treated


title: day6_ctrl_279

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW39


title: MP-37, condition7-Rifampicine treated


title: MP-35, condition7-Rifampicine treated


title: day6_ctrl_275

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW35


title: day6_ctrl_276

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW36


title: day6_ctrl_278

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW38


title: day6_ctrl_280

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW40


title: MP-32, condition7-Rifampicine treated


title: MP-34, condition7-Rifampicine treated


title: MP-31, condition7-Rifampicine treated


title: MP-50, condition7-Rifampicine treated


title: day6_ctrl_272

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW32


title: day6_ctrl_273

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW33


title: MP-30, condition7-Rifampicine treated


title: day6_ctrl_271

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW31


title: MP-29, condition7-Rifampicine treated


title: MP-3, condition7-Rifampicine treated


title: MP-41, condition7-Rifampicine treated


title: MP-27, condition7-Rifampicine treated


title: day6_ctrl_268

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW28


title: MP-28, condition7-Rifampicine treated


title: day6_ctrl_269

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW29


title: day6_ctrl_267

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW27


title: day6_ctrl_270

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW30


title: day6_ctrl_266

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW26


title: day6_ctrl_265

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW25


title: MP-26, condition7-Rifampicine treated

description: condition7_Rifampicine_expression_tmm_normalization_exp.txt


title: day6_ctrl_264

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW24


title: day6_ctrl_277

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW37


title: day6_ctrl_274

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW34


title: MP-24, condition7-Rifampicine treated


title: MP-21, condition7-Rifampicine treated


title: day6_ctrl_263

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW23


title: day6_ctrl_262

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW22


title: day6_ctrl_261

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW21


title: MP-18, condition7-Rifampicine treated


title: day6_ctrl_260

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW20


title: MP-20, condition7-Rifampicine treated


title: day6_ctrl_259

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW19


title: MP-2, condition7-Rifampicine treated


title: MP-15, condition7-Rifampicine treated


title: MP-16, condition7-Rifampicine treated


title: day6_ctrl_258

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW18


title: day6_ctrl_283

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC464_ROW03


title: MP-12, condition7-Rifampicine treated


title: MP-1, condition7-Rifampicine treated


title: day6_ctrl_257

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW17


title: MP-25, condition7-Rifampicine treated


title: day6_ctrl_255

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW15


title: day6_ctrl_256

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW16


title: day6_ctrl_253

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW13


title: day6_ctrl_252

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW12


title: day6_ctrl_254

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW14


title: day6_ctrl_251

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW11


title: day6_ctrl_249

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW09


title: day6_ctrl_250

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW10


title: MP-14, condition7-Rifampicine treated

description: condition7_Rifampicine_expression_tmm_normalization_exp.txt


title: MP-50, condition6-Phenytoin treated

description: condition6_Phenytoin_expression_tmm_normalization_exp.txt

value: Phenytoin drug


title: MP-49, condition6-Phenytoin treated


title: day6_ctrl_248

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW08


title: day6_ctrl_247

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW07


title: MP-52, condition6-Phenytoin treated


title: day6_ctrl_246

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW06


title: MP-41, condition6-Phenytoin treated


title: MP-43, condition6-Phenytoin treated


title: MP-44, condition6-Phenytoin treated


title: day6_ctrl_245

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW05


title: MP-40, condition6-Phenytoin treated


title: MP-39, condition6-Phenytoin treated


title: day6_ctrl_244

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW04


title: MP-37, condition6-Phenytoin treated


title: day6_ctrl_243

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW03


title: day6_ctrl_241

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW01


title: MP-0, condition7-Rifampicine treated


title: day6_ctrl_242

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC463_ROW02


title: MP-51, condition6-Phenytoin treated


title: MP-34, condition6-Phenytoin treated


title: MP-32, condition6-Phenytoin treated


title: day6_ctrl_239

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW39


title: MP-45, condition6-Phenytoin treated


title: MP-31, condition6-Phenytoin treated


title: day6_ctrl_238

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW38


title: MP-30, condition6-Phenytoin treated


title: MP-42, condition6-Phenytoin treated


title: MP-3, condition6-Phenytoin treated


title: day6_ctrl_237

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW37


title: MP-35, condition6-Phenytoin treated


title: day6_ctrl_236

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW36


title: day6_ctrl_235

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW35


title: MP-28, condition6-Phenytoin treated


title: MP-29, condition6-Phenytoin treated


title: day6_ctrl_234

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW34


title: day6_ctrl_232

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW32


title: MP-26, condition6-Phenytoin treated


title: day6_ctrl_233

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW33


title: MP-24, condition6-Phenytoin treated

description: condition6_Phenytoin_expression_tmm_normalization_exp.txt


title: MP-25, condition6-Phenytoin treated


title: MP-21, condition6-Phenytoin treated


title: MP-27, condition6-Phenytoin treated


title: day6_ctrl_230

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW30


title: day6_ctrl_231

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW31


title: day6_ctrl_228

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW28


title: MP-2, condition6-Phenytoin treated


title: MP-18, condition6-Phenytoin treated


title: day6_ctrl_229

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW29


title: day6_ctrl_227

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW27


title: day6_ctrl_240

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW40


title: day6_ctrl_226

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW26


title: MP-15, condition6-Phenytoin treated


title: MP-16, condition6-Phenytoin treated


title: day6_ctrl_224

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW24


title: day6_ctrl_225

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW25


title: day6_ctrl_223

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW23


title: MP-12, condition6-Phenytoin treated


title: MP-14, condition6-Phenytoin treated


title: MP-1, condition6-Phenytoin treated


title: day6_ctrl_222

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW22


title: day6_ctrl_221

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW21


title: day6_ctrl_219

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW19


title: day6_ctrl_220

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW20


title: MP-52, condition5-Carbamazepine treated

description: condition5_Carbamazepine_expression_tmm_normalization_exp.txt

value: Carbamazepine drug


title: MP-50, condition5-Carbamazepine treated


title: MP-0, condition6-Phenytoin treated


title: day6_ctrl_218

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW18


title: MP-20, condition6-Phenytoin treated

description: condition6_Phenytoin_expression_tmm_normalization_exp.txt


title: MP-51, condition5-Carbamazepine treated


title: MP-49, condition5-Carbamazepine treated


title: MP-44, condition5-Carbamazepine treated


title: day6_ctrl_215

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW15


title: MP-43, condition5-Carbamazepine treated


title: MP-42, condition5-Carbamazepine treated


title: day6_ctrl_213

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW13


title: MP-41, condition5-Carbamazepine treated


title: day6_ctrl_212

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW12


title: day6_ctrl_211

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW11


title: MP-39, condition5-Carbamazepine treated


title: day6_ctrl_210

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW10


title: day6_ctrl_209

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW09


title: MP-37, condition5-Carbamazepine treated


title: day6_ctrl_217

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW17


title: day6_ctrl_206

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW06


title: MP-34, condition5-Carbamazepine treated


title: MP-35, condition5-Carbamazepine treated


title: day6_ctrl_207

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW07


title: day6_ctrl_208

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW08


title: day6_ctrl_203

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW03


title: day6_ctrl_216

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW16


title: day6_ctrl_204

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW04


title: MP-28, condition5-Carbamazepine treated


title: MP-45, condition5-Carbamazepine treated


title: day6_ctrl_205

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW05


title: MP-29, condition5-Carbamazepine treated

description: condition5_Carbamazepine_expression_tmm_normalization_exp.txt


title: MP-31, condition5-Carbamazepine treated


title: day6_ctrl_202

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW02


title: MP-32, condition5-Carbamazepine treated


title: MP-27, condition5-Carbamazepine treated


title: day6_ctrl_214

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW14


title: day6_ctrl_200

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW40


title: MP-3, condition5-Carbamazepine treated


title: day6_ctrl_201

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC462_ROW01


title: MP-40, condition5-Carbamazepine treated


title: MP-26, condition5-Carbamazepine treated


title: MP-25, condition5-Carbamazepine treated


title: day6_ctrl_199

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW39


title: MP-24, condition5-Carbamazepine treated


title: day6_ctrl_198

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW38


title: MP-21, condition5-Carbamazepine treated


title: MP-20, condition5-Carbamazepine treated


title: MP-2, condition5-Carbamazepine treated


title: MP-15, condition5-Carbamazepine treated


title: MP-16, condition5-Carbamazepine treated


title: MP-14, condition5-Carbamazepine treated


title: day6_ctrl_192

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW32


title: MP-18, condition5-Carbamazepine treated


title: day6_ctrl_194

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW34


title: day6_ctrl_197

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW37


title: day6_ctrl_190

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW30


title: day6_ctrl_195

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW35


title: day6_ctrl_196

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW36


title: day6_ctrl_193

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW33


title: MP-0, condition5-Carbamazepine treated


title: day6_ctrl_191

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW31


title: day6_ctrl_188

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW28


title: MP-1, condition5-Carbamazepine treated


title: day6_ctrl_186

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW26


title: day6_ctrl_187

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW27


title: day6_ctrl_185

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW25


title: day6_ctrl_184

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW24


title: day6_ctrl_183

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW23


title: MP-45, condition4-Dexamethasone treated

description: condition4_Dexamethasone_expression_tmm_normalization_exp.txt

value: Dexamethasone drug


title: MP-52, condition4-Dexamethasone treated


title: MP-51, condition4-Dexamethasone treated


title: MP-50, condition4-Dexamethasone treated


title: MP-49, condition4-Dexamethasone treated


title: MP-44, condition4-Dexamethasone treated


title: day6_ctrl_189

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW29


title: MP-43, condition4-Dexamethasone treated


title: MP-12, condition5-Carbamazepine treated

description: condition5_Carbamazepine_expression_tmm_normalization_exp.txt


title: day6_ctrl_178

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW18


title: MP-42, condition4-Dexamethasone treated


title: day6_ctrl_180

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW20


title: MP-40, condition4-Dexamethasone treated


title: day6_ctrl_181

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW21


title: day6_ctrl_177

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW17


title: MP-41, condition4-Dexamethasone treated


title: day6_ctrl_175

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW15


title: day6_ctrl_176

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW16


title: MP-39, condition4-Dexamethasone treated


title: day6_ctrl_179

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW19


title: day6_ctrl_173

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW13


title: day6_ctrl_174

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW14


title: MP-32, condition4-Dexamethasone treated


title: MP-31, condition4-Dexamethasone treated


title: MP-37, condition4-Dexamethasone treated


title: day6_ctrl_182

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW22


title: day6_ctrl_169

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW09


title: day6_ctrl_171

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW11


title: MP-34, condition4-Dexamethasone treated


title: MP-30, condition4-Dexamethasone treated


title: MP-29, condition4-Dexamethasone treated


title: day6_ctrl_172

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW12


title: day6_ctrl_170

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW10


title: MP-3, condition4-Dexamethasone treated

description: condition4_Dexamethasone_expression_tmm_normalization_exp.txt


title: MP-28, condition4-Dexamethasone treated


title: day6_ctrl_168

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW08


title: day6_ctrl_167

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW07


title: MP-35, condition4-Dexamethasone treated


title: day6_ctrl_165

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW05


title: day6_ctrl_164

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW04


title: day6_ctrl_163

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW03


title: MP-21, condition4-Dexamethasone treated


title: MP-26, condition4-Dexamethasone treated


title: day6_ctrl_166

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW06


title: MP-24, condition4-Dexamethasone treated


title: MP-25, condition4-Dexamethasone treated


title: MP-20, condition4-Dexamethasone treated


title: day6_ctrl_162

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW02


title: day6_ctrl_160

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW40


title: MP-18, condition4-Dexamethasone treated


title: MP-16, condition4-Dexamethasone treated


title: day6_ctrl_159

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW39


title: MP-15, condition4-Dexamethasone treated


title: day6_ctrl_158

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW38


title: MP-14, condition4-Dexamethasone treated


title: day6_ctrl_156

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW36


title: MP-27, condition4-Dexamethasone treated


title: day6_ctrl_157

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW37


title: MP-1, condition4-Dexamethasone treated


title: day6_ctrl_154

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW34


title: MP-12, condition4-Dexamethasone treated


title: MP-52, condition3-Phenobarbital treated

description: condition3_Phenobarbital_expression_tmm_normalization_exp.txt

value: Phenobarbital drug


title: day6_ctrl_153

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW33

value: basilar papillae


title: MP-51, condition3-Phenobarbital treated


title: MP-2, condition4-Dexamethasone treated


title: day6_ctrl_150

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW30


title: day6_ctrl_161

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC461_ROW01


title: MP-50, condition3-Phenobarbital treated


title: day6_ctrl_151

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW31


title: MP-49, condition3-Phenobarbital treated


title: day6_ctrl_149

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW29


title: MP-44, condition3-Phenobarbital treated


title: day6_ctrl_146

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW26


title: MP-0, condition4-Dexamethasone treated

description: condition4_Dexamethasone_expression_tmm_normalization_exp.txt


title: day6_ctrl_148

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW28


title: MP-43, condition3-Phenobarbital treated


title: MP-45, condition3-Phenobarbital treated


title: day6_ctrl_147

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW27


title: day6_ctrl_155

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW35


title: MP-40, condition3-Phenobarbital treated


title: MP-41, condition3-Phenobarbital treated


title: day6_ctrl_145

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW25


title: day6_ctrl_144

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW24


title: MP-42, condition3-Phenobarbital treated


title: MP-39, condition3-Phenobarbital treated


title: day6_ctrl_143

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW23


title: MP-37, condition3-Phenobarbital treated


title: day6_ctrl_142

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW22


title: day6_ctrl_141

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW21


title: day6_ctrl_152

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW32


title: MP-34, condition3-Phenobarbital treated

description: condition3_Phenobarbital_expression_tmm_normalization_exp.txt


title: day6_ctrl_140

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW20


title: day6_ctrl_138

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW18


title: day6_ctrl_139

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW19


title: MP-32, condition3-Phenobarbital treated


title: MP-31, condition3-Phenobarbital treated


title: day6_ctrl_137

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW17


title: day6_ctrl_136

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW16


title: MP-29, condition3-Phenobarbital treated


title: MP-28, condition3-Phenobarbital treated


title: day6_ctrl_135

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW15


title: MP-27, condition3-Phenobarbital treated


title: day6_ctrl_132

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW12


title: MP-26, condition3-Phenobarbital treated


title: day6_ctrl_131

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW11


title: day6_ctrl_133

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW13


title: MP-35, condition3-Phenobarbital treated


title: day6_ctrl_130

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW10


title: day6_ctrl_129

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW09


title: MP-20, condition3-Phenobarbital treated


title: day6_ctrl_128

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW08


title: MP-2, condition3-Phenobarbital treated


title: MP-21, condition3-Phenobarbital treated


title: MP-24, condition3-Phenobarbital treated


title: MP-25, condition3-Phenobarbital treated


title: day6_ctrl_126

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW06


title: day6_ctrl_127

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW07


title: MP-16, condition3-Phenobarbital treated


title: MP-3, condition3-Phenobarbital treated


title: MP-18, condition3-Phenobarbital treated


title: MP-30, condition3-Phenobarbital treated


title: MP-15, condition3-Phenobarbital treated


title: day6_ctrl_125

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW05


title: day6_ctrl_134

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW14


title: MP-14, condition3-Phenobarbital treated

description: condition3_Phenobarbital_expression_tmm_normalization_exp.txt


title: day6_ctrl_123

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW03


title: MP-12, condition3-Phenobarbital treated


title: day6_ctrl_124

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW04


title: day6_ctrl_120

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW40


title: day6_ctrl_121

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW01


title: day6_ctrl_119

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW39


title: day6_ctrl_118

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW38


title: MP-52, condition2-Omeprazole treated

description: condition2_Omeprazole_expression_tmm_normalization_exp.txt

value: Omeprazole drug


title: MP-0, condition3-Phenobarbital treated


title: MP-1, condition3-Phenobarbital treated


title: MP-51, condition2-Omeprazole treated


title: day6_ctrl_117

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW37

value: 144-h culture


title: MP-44, condition2-Omeprazole treated


title: day6_ctrl_114

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW34


title: day6_ctrl_116

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW36


title: MP-45, condition2-Omeprazole treated


title: day6_ctrl_115

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW35


title: MP-49, condition2-Omeprazole treated


title: day6_ctrl_112

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW32


title: day6_ctrl_111

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW31


title: MP-41, condition2-Omeprazole treated


title: MP-42, condition2-Omeprazole treated


title: day6_ctrl_113

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW33


title: MP-43, condition2-Omeprazole treated


title: MP-40, condition2-Omeprazole treated


title: day6_ctrl_122

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC460_ROW02


title: MP-39, condition2-Omeprazole treated


title: day6_ctrl_108

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW28


title: MP-35, condition2-Omeprazole treated


title: MP-37, condition2-Omeprazole treated


title: day6_ctrl_110

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW30


title: MP-50, condition2-Omeprazole treated


title: day6_ctrl_107

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW27


title: day6_ctrl_106

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW26


title: day6_ctrl_109

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW29


title: MP-34, condition2-Omeprazole treated


title: MP-31, condition2-Omeprazole treated


title: MP-32, condition2-Omeprazole treated


title: day6_ctrl_104

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW24


title: day6_ctrl_103

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW23


title: MP-3, condition2-Omeprazole treated


title: day6_ctrl_102

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW22


title: day6_ctrl_101

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW21


title: day6_ctrl_100

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW20


title: MP-29, condition2-Omeprazole treated

description: condition2_Omeprazole_expression_tmm_normalization_exp.txt


title: MP-27, condition2-Omeprazole treated


title: day6_ctrl_098

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW18


title: MP-25, condition2-Omeprazole treated


title: day6_ctrl_099

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW19


title: MP-26, condition2-Omeprazole treated


title: day6_ctrl_097

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW17


title: MP-24, condition2-Omeprazole treated


title: day6_ctrl_096

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW16


title: MP-21, condition2-Omeprazole treated


title: day6_ctrl_105

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW25


title: MP-20, condition2-Omeprazole treated


title: day6_ctrl_090

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW10


title: MP-12, condition2-Omeprazole treated


title: day6_ctrl_089

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW09


title: day6_ctrl_093

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW13


title: MP-18, condition2-Omeprazole treated


title: MP-14, condition2-Omeprazole treated


title: MP-15, condition2-Omeprazole treated


title: MP-2, condition2-Omeprazole treated


title: day6_ctrl_092

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW12


title: day6_ctrl_087

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW07


title: day6_ctrl_095

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW15


title: MP-30, condition2-Omeprazole treated


title: CCX250

first: Mohamed

last: Abazeed

state: IL

address: 303 E Superior St Lurie

department: Radiation Oncology

description: single tumor, homogenized, grown in reduced serum to derive the an ex vivo culture to maintian all cell populations

data_processing:
Cell Ranger version 3.0.2 was used to convert Illumina base call files to FASTQ files, which were aligned to the hg19 human reference genome and transcriptome provided by 10x Genomics.
Gene read counts were normalized by calculating transcripts per million (TPM)
Assembly: hg19

source_name: NSG mice

growth_protocol: All ex vivo lines were grown in Advanced RPMI under low serum condiations for atleast 12 weeks.

extract_protocol:
RNA was isolated from single cells using gel beads with barcodes using chromium'3 10X kit
Single cells were processed through the 10X Chromium 3’ Single Cell Platform using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA), following the manufacturer’s protocol for library construction.

value: human-derived xenograft ex vivo line

value: small cell lung carcinoma

tag: passages

value: 12 weeks post derivation from the xenograft


title: day6_ctrl_088

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW08


title: day6_ctrl_086

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW06


title: day6_ctrl_094

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW14


title: MP-28, condition2-Omeprazole treated


title: CBX163


title: day6_ctrl_084

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW04


title: CBX110


title: day6_ctrl_083

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW03


title: CBX119


title: day6_ctrl_082

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW02


title: MP-16, condition2-Omeprazole treated

description: condition2_Omeprazole_expression_tmm_normalization_exp.txt


title: day6_ctrl_091

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW11


title: MP-1, condition2-Omeprazole treated


title: CCX1


title: day6_ctrl_080

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW40


title: CBX140


title: day6_ctrl_081

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW01


title: gdT, TGFB, resting, 1

city: Solna

first: Chirine

last: RAFIA

address: Bioclinicum

department: Medicin Solna

country: Sweden

institute: Karolinska Institutet

data_processing:
All sixteen bases of the first read (from the read pairs) must have quality scores of at least 10 and the first six bases must correspond exactly to a designed well-specific barcode.
The second reads were aligned to RefSeq human mRNA sequences (hg19) using bwa version 0.7.4 4
bam alignment files obtained from bwa. Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 14936 genes detected.
Assembly: hg19
Supplementary files format and content: diffexpr-GD_none_TGF.csv

source_name: peripheral blood

growth_protocol: Samples were growth in IMDM supplemented with 10% serum, penicillin, streptomycine, glutamine

extract_protocol:
All samples were stored at -80C. Total RNA extraction using RNeasy mini kit (Qiagen) according to the manufacturer's instructions. The quality of RNA was controlled by an Agilent 2100 Bioanalyzer. RNAs were qualified if the 28S/18S ratio was more than 1.5.
Libraries were prepared from 10 ng of total RNA. The mRNA poly(A) tail was tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during template-switching reverse transcriptase. Barcoded cDNAs from multiple samples were then pooled, amplified and tagmented using a transposon-fragmentation approach that enriches for 3’ends of cDNA. A library of 350-800 bp was run on an Illumina HiSeq 2500 using a TruSeq Rapid SBS Kit (Illumina, San Diego, CA, USA)
3' sequencing RNA
3'-DGE-Seq

treatment_protocol: Cells were treated or not with 10ng/mL TGF-b and incubated for 3 days. Cells were activated or not using BrHPP for 4h prior to extraction.

value: peripheral blood

value: Vg9Vd2 T cells

value: TGF-b (10ng/mL)


title: gdT, TGFB, resting, 2


title: gdT, TGFB, activated, 2

value: TGF-b (10ng/mL), BrHPP


title: day6_ctrl_085

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC459_ROW05


title: MP-0, condition2-Omeprazole treated

value: liver hepatocyte cells


title: gdT, TGFB, resting, 3


title: day6_ctrl_078

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW38


title: day6_ctrl_076

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW36


title: gdT, TGFB, activated, 1


title: day6_ctrl_077

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW37


title: day6_ctrl_075

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW35


title: day6_ctrl_072

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW32


title: day6_ctrl_079

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW39


title: gdT, none, resting, 2


title: gdT, none, resting, 1


title: gdT, none, activated, 2

value: BrHPP


title: gdT, none, resting, 3


title: day6_ctrl_073

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW33


title: day6_ctrl_071

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW31


title: gdT, none, activated, 3


title: day6_ctrl_069

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW29


title: gdT, none, activated, 1


title: day6_ctrl_070

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW30


title: day6_ctrl_068

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW28


title: day6_ctrl_074

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW34


title: MP-90, condition7-Rifampicine treated

description: condition7_Rifampicine_expression_tmm_normalization_exp.txt

value: Male

value: Rifampicine drug


title: gdT, TGFB, activated, 3


title: day6_ctrl_067

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW27


title: day6_ctrl_066

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW26


title: MP-78, condition7-Rifampicine treated


title: day6_ctrl_063

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW23


title: MP-77, condition7-Rifampicine treated

value: Female


title: MP-70, condition7-Rifampicine treated


title: day6_ctrl_064

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW24


title: day6_ctrl_062

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW22


title: MP-76, condition7-Rifampicine treated


title: day6_ctrl_061

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW21


title: MP-9, condition7-Rifampicine treated


title: day6_ctrl_059

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW19


title: day6_ctrl_065

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW25


title: MP-69, condition7-Rifampicine treated


title: MP-68, condition7-Rifampicine treated


title: day6_ctrl_060

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW20


title: MP-7, condition7-Rifampicine treated


title: day6_ctrl_056

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW16


title: day6_ctrl_057

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW17


title: MP-75, condition7-Rifampicine treated


title: MP-67, condition7-Rifampicine treated


title: day6_ctrl_055

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW15


title: MP-66, condition7-Rifampicine treated


title: day6_ctrl_054

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW14


title: MP-65, condition7-Rifampicine treated


title: day6_ctrl_053

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW13


title: MP-63, condition7-Rifampicine treated


title: MP-64, condition7-Rifampicine treated


title: MP-8, condition7-Rifampicine treated


title: MP-62, condition7-Rifampicine treated


title: day6_ctrl_050

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW10


title: day6_ctrl_052

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW12


title: day6_ctrl_049

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW09


title: MP-60, condition7-Rifampicine treated

description: condition7_Rifampicine_expression_tmm_normalization_exp.txt


title: day6_ctrl_048

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW08


title: MP-6, condition7-Rifampicine treated


title: MP-59, condition7-Rifampicine treated


title: MP-57, condition7-Rifampicine treated


title: MP-58, condition7-Rifampicine treated


title: day6_ctrl_044

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW04


title: MP-54, condition7-Rifampicine treated


title: day6_ctrl_046

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW06


title: MP-55, condition7-Rifampicine treated


title: day6_ctrl_042

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW02


title: MP-90, condition6-Phenytoin treated

description: condition6_Phenytoin_expression_tmm_normalization_exp.txt

value: Phenytoin drug


title: day6_ctrl_045

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW05


title: MP-9, condition6-Phenytoin treated


title: day6_ctrl_040

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW40


title: day6_ctrl_047

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW07


title: MP-61, condition7-Rifampicine treated


title: MP-53, condition7-Rifampicine treated


title: MP-78, condition6-Phenytoin treated


title: day6_ctrl_038

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW38


title: day6_ctrl_041

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW01


title: MP-77, condition6-Phenytoin treated


title: MP-8, condition6-Phenytoin treated


title: MP-75, condition6-Phenytoin treated


title: MP-76, condition6-Phenytoin treated


title: day6_ctrl_036

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW36


title: day6_ctrl_037

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW37


title: day6_ctrl_035

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW35


title: day6_ctrl_043

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW03


title: day6_ctrl_034

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW34


title: day6_ctrl_051

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW11


title: MP-69, condition6-Phenytoin treated


title: day6_ctrl_031

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW31


title: day6_ctrl_032

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW32


title: day6_ctrl_030

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW30


title: MP-7, condition6-Phenytoin treated


title: MP-65, condition6-Phenytoin treated


title: MP-68, condition6-Phenytoin treated


title: MP-67, condition6-Phenytoin treated


title: day6_ctrl_039

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW39


title: day6_ctrl_033

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW33


title: day6_ctrl_028

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW28


title: MP-64, condition6-Phenytoin treated

description: condition6_Phenytoin_expression_tmm_normalization_exp.txt


title: MP-63, condition6-Phenytoin treated


title: day6_ctrl_026

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW26


title: MP-62, condition6-Phenytoin treated


title: MP-60, condition6-Phenytoin treated


title: day6_ctrl_029

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW29


title: MP-58, condition6-Phenytoin treated


title: day6_ctrl_023

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW23


title: MP-57, condition6-Phenytoin treated


title: day6_ctrl_022

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW22


title: day6_ctrl_024

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW24


title: MP-66, condition6-Phenytoin treated


title: MP-55, condition6-Phenytoin treated


title: MP-54, condition6-Phenytoin treated


title: day6_ctrl_058

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC458_ROW18


title: day6_ctrl_025

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW25


title: MP-53, condition6-Phenytoin treated


title: day6_ctrl_020

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW20


title: day6_ctrl_018

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW18


title: day6_ctrl_019

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW19


title: day6_ctrl_021

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW21


title: MP-90, condition5-Carbamazepine treated

description: condition5_Carbamazepine_expression_tmm_normalization_exp.txt

value: Carbamazepine drug


title: day6_ctrl_016

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW16

value: basilar papillae


title: day6_ctrl_027

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW27


title: day6_ctrl_015

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW15


title: MP-8, condition5-Carbamazepine treated


title: MP-9, condition5-Carbamazepine treated


title: MP-78, condition5-Carbamazepine treated


title: day6_ctrl_014

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW14


title: day6_ctrl_017

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW17


title: MP-76, condition5-Carbamazepine treated


title: MP-77, condition5-Carbamazepine treated


title: day6_ctrl_013

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW13


title: day6_ctrl_012

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW12


title: MP-59, condition6-Phenytoin treated

description: condition6_Phenytoin_expression_tmm_normalization_exp.txt


title: day6_ctrl_010

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW10


title: MP-6, condition6-Phenytoin treated


title: MP-75, condition5-Carbamazepine treated


title: day6_ctrl_009

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW09


title: MP-7, condition5-Carbamazepine treated


title: day6_ctrl_008

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW08


title: MP-69, condition5-Carbamazepine treated


title: MP-70, condition5-Carbamazepine treated


title: MP-68, condition5-Carbamazepine treated


title: day6_ctrl_006

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW06


title: MP-65, condition5-Carbamazepine treated


title: MP-67, condition5-Carbamazepine treated


title: day6_ctrl_004

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW04


title: day6_ctrl_003

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW03


title: MP-64, condition5-Carbamazepine treated


title: day6_ctrl_001

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW01


title: MP-62, condition5-Carbamazepine treated


title: MP-63, condition5-Carbamazepine treated


title: day6_ctrl_002

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW02


title: MP-61, condition5-Carbamazepine treated

description: condition5_Carbamazepine_expression_tmm_normalization_exp.txt


title: MP-60, condition5-Carbamazepine treated